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wuka (guest) 30 Oct 2017 16:12
in discussion Hidden / Per page discussions » Analyze and Optimize a peptide with TINKER

Hi, I'm trying to do a MD simulation of a protein with Tinker.
But I don't know how to do the equalization for the systems. I saw some tutorial that first do a minimization of the system and then increase the temperature slowly. But I didn't find out something similar to Charmm or NAMD where we first constrain the system with a high constrain force, and then decrease this constrains step by step. Are there some simulation key word for this in Tinker. Are there a standard way for do the equalibration of protein before run the MD simulations. Thanks a lot.

Wuka

by wuka (guest), 30 Oct 2017 16:12
Chinmoy Basak (guest) 30 Oct 2017 07:07
in discussion Hidden / Per page discussions » Modeling Carbon Nanotubes with GROMACS

Hi,

Can you please answer this question.

How Gromacs differentiate same atom pairs and bond length having different charges from info in Pdb files? For example?
For example OH of carboxyl group and Phenolic OH group has same atoms and bond length but slightly different charges.

by Chinmoy Basak (guest), 30 Oct 2017 07:07
meiting (guest) 23 Oct 2017 13:55
in discussion Hidden / Per page discussions » TINKER explained

Dear all,
I used xyzedit to build a solvent box of cyclohexane.
I used the xyz file in the /tinker/example/ with the amoeba09.prm.
The ncopy =3765 and x,y,z is 33 33 33.
However, when the parameters of torsion is printing, the program stopped and the error read that: "TINKER is Unable to Continue; Terminating the Current Calculation."
I want to know why. I read the code of xyzedit.f but I did not find the reason.
Thanks for your time,
Best Regards,
Meiting Wang

by meiting (guest), 23 Oct 2017 13:55
Shivani Gup[ta (guest) 07 Aug 2017 06:06
in discussion Hidden / Per page discussions » Accelrys Materials Studio

I have a file in perl scirpt .I want to know how to define box size in the script.
need your help please,…

Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 259.
Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 260.

#!/usr/bin/perl -w

  1. Rounding procedure of the mighty PerlMonks…
  2. Halleluja!

sub round {
my( $num, $prec )= @_;
return int( $num/$prec + 0.5 - ($num<0) ) * $prec;
}

  1. Procedure to calculate the distance between 2 Vectors

sub abstand {
my( $a1,$a2,$a3,$b1,$b2,$b3)= @_;
return ( (($a1-$b1)2 + ($a2-$b2)2 + ($a3-$b3)2)0.5);
}

#Check input

if (@ARGV<7) {die "\n\n
###########################################################################
INFLATEGRO
Written by Christian Kandt, (c) 2005-2007

Kandt C, Ash WL, Tieleman DP (2007): Setting up and running molecular
dyanmics simulations of membrane proteins. Methods 41:475-488

###########################################################################

INFLATEGRO reads the coordinates of a bilayer and inflates them
in XY directions using a common scaling factor. To identify
the lipids their actual residue name must be given.

Water coordinates (SOL) will be ingored, everything else will
be centered in the XY plane of the new simulation box.

A distance cutoff in A can be defined: Only lipids with a
P - CA distance exceeding that cutoff will be written. It is currently
assumed that you're actually dealing with phospholipids. However, this can
be easily extended. Just have a look at the code.

Area per lipid is estimated by caculating the area per protein first.
This is done using a grid-based approach. A grid size of 5 A was found to
give good results. Output is written as a 3-collumned ASCII file holding
3 area per lipid values: total, upper leaflet & lower leaflet.

If the additional flag >protein< is set only the protein
coordinates will be written.

USAGE:


INFLATEGRO bilayer.gro scaling_factor lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat (protein)

…good luck!

;) Christian Kandt 05/2007

\n\n";}

if (!(open (INPUT, $ARGV[0]))) {print "Eeeeek! No $ARGV[0] at all!\n\n";
die;}

  1. Read lipid coordinates

#$input=$ARGV[0];
$scale=$ARGV[1];
$name=$ARGV[2];
$cutoff=$ARGV[3]*0.1;
$output=$ARGV[4];
$gridsize=$ARGV[5];
$area=$ARGV[6];

$switch=0;

if (@ARGV==8 and $ARGV[7] eq "protein") {
print "Well, just the protein then….\n";
$switch=1;
}

$zaehler=1;
$counter=1;
$now=0;
$protein_xmax=-1000;
$protein_ymax=-1000;
$protein_xmin=1000;
$protein_ymin=1000;

print STDOUT "Reading….. \n";
while (<INPUT>) {

if (/^ +([0-9.-]+) +([0-9.-]+) +([0-9.-]+)/) {
$box_x=$1;
$box_y=$2;
$box_z=$3;
}

unless ($now==0) {

if (/^ +(\d+)(\S+) +(\S+) +([0-9.-]+) +([0-9.-]+) +([0-9.-]+)/ ) {

if ($2 eq $name) {
$resnum_l[$zaehler]=$1;
$resname_l[$zaehler]=$2;
$atmnamenum=$3;
$x_l[$zaehler]=$4;
$y_l[$zaehler]=$5;
$z_l[$zaehler]=$6;

$howlong=length($atmnamenum) - 1;
$atmname_l[$zaehler]=substr($atmnamenum,0,$howlong-4);
$atmnum_l[$zaehler]=substr($atmnamenum,$howlong-4);

#print "$resnum_l[$zaehler]: $atmnamenum $atmname_l[$zaehler] $atmnum_l[$zaehler]\n";
$zaehler++;
}

if (!($2 eq $name) && !($2 eq "SOL")) {
$resnum_p[$counter]=$1;
$resname_p[$counter]=$2;
$atmnamenum=$3;
$x_p[$counter]=$4;
$y_p[$counter]=$5;
$z_p[$counter]=$6;

$howlong=length($atmnamenum) - 1;
$atmname_p[$counter]=substr($atmnamenum,0,$howlong-4);
$atmnum_p[$counter]=substr($atmnamenum,$howlong-4);

if ($x_p[$counter]>$protein_xmax) {$protein_xmax=$x_p[$counter];}
if ($x_p[$counter]<$protein_xmin) {$protein_xmin=$x_p[$counter];}
if ($y_p[$counter]>$protein_ymax) {$protein_ymax=$y_p[$counter];}
if ($y_p[$counter]<$protein_ymin) {$protein_ymin=$y_p[$counter];}

#print "$resnum_p[$counter]: $atmnamenum $atmname_p[$counter] $atmnum_p[$counter]\n";
$counter++;
}

}

}

if (/^ +(\d+)(\S+) +(\S+) +(\d+) +([0-9.-]+) +([0-9.-]+) +([0-9.-]+)/ ) {

if ($2 eq $name) {
$resnum_l[$zaehler]=$1;
$resname_l[$zaehler]=$2;
$atmname_l[$zaehler]=$3;
$atmnum_l[$zaehler]=$4;
$x_l[$zaehler]=$5;
$y_l[$zaehler]=$6;
$z_l[$zaehler]=$7;

if ($atmnum_l[$zaehler]==9999) {$now=1;}
#print "$resnum_l[$zaehler] $now\n";
$zaehler++;

}

if (!($2 eq $name) && !($2 eq "SOL")) {
$resnum_p[$counter]=$1;
$resname_p[$counter]=$2;
$atmname_p[$counter]=$3;
$atmnum_p[$counter]=$4;
$x_p[$counter]=$5;
$y_p[$counter]=$6;
$z_p[$counter]=$7;

if ($x_p[$counter]>$protein_xmax) {$protein_xmax=$x_p[$counter];}
if ($x_p[$counter]<$protein_xmin) {$protein_xmin=$x_p[$counter];}
if ($y_p[$counter]>$protein_ymax) {$protein_ymax=$y_p[$counter];}
if ($y_p[$counter]<$protein_ymin) {$protein_ymin=$y_p[$counter];}

if ($atmnum_p[$counter]==9999) {$now=1;}
#print "$resnum_p[$counter] \n";
$counter++;
}

}

}

close (INPUT);

$zaehler;
$counter
;

$totalatmn=$zaehler+$counter;

  1. Converting nm into A

$protein_xmin=$protein_xmin*10;
$protein_xmax=$protein_xmax*10;
$protein_ymin=$protein_ymin*10;
$protein_ymax=$protein_ymax*10;

  1. New boxsize

$box_x=$box_x*$scale;
$box_y=$box_y*$scale;

  1. Scaling P positions & calculating translation vector

print STDOUT "Scaling lipids….\n";

$pcount=1;

for ($k=1; $k<=$zaehler; $k++) {

if (substr($atmname_l[$k],0,1) eq "P") {

$pxneu=$x_l[$k]*$scale;
$pyneu=$y_l[$k]*$scale;

$res=$resnum_l[$k];
$translatex_l[$res]=$pxneu-$x_l[$k];
$translatey_l[$res]=$pyneu-$y_l[$k];

  1. $phos_x[$pcount]=$x_l[$k]+$translatex_l[$res];
  2. $phos_y[$pcount]=$y_l[$k]+$translatey_l[$res];

$phosz[$pcount]=$z_l[$k];
$pcount++;
}
}

$pcount—;

print "There are $pcount lipids…\n";

$atomperlipid= $zaehler/$pcount;

print "with $atomperlipid atoms per lipid..\n";

  1. Determination of upper & lower leaflet

print "\nDetermining upper and lower leaflet…\n";

$middle=0;

for ($p=1;$p<=$pcount; $p++) {

$middle=$middle + $phosz[$p];

}

$middle=$middle / $pcount;

$uppercount=0;
$lowercount=0;
$upper=0;
$lower=0;

for ($p=1;$p<=$pcount; $p++) {

if ($phosz[$p]>$middle) {$upper=$upper+$phosz[$p];
$uppercount++;}
if ($phosz[$p]<$middle) {$lower=$lower+$phosz[$p];
$lowercount++;}

}
$upper=$upper/$uppercount;
$lower=$lower/$lowercount;

print "$uppercount lipids in the upper…\n";
print "$lowercount lipids in the lower leaflet \n\n";

#Determining protein XY-COM & calculating translation vector

if ($counter==0) {print "No protein coordinates found…\n";}
if ($counter>0) {

print STDOUT "Centering protein….\n";

$xpsum=0;
$ypsum=0;

for ($k=1; $k<=$counter; $k++) {
$xpsum=$xpsum+$x_p[$k];
$ypsum=$ypsum+$y_p[$k];
}

$xcom=$xpsum/$counter;
$ycom=$ypsum/$counter;

$xcenter=0.5*$box_x;
$ycenter=0.5*$box_y;

$translatex_p=$xcenter - $xcom;
$translatey_p=$ycenter - $ycom;

#print "COM: $xcom $ycom\n";
#print "New center: $xcenter $ycenter\n";
#print "Translation vector: $translatex_p $translatey_p\n\n";

}

  1. Checking for protein lipid overlap

$upper_rm=0;
$lower_rm=0;

if ($cutoff>0) {
if ($switch==0) {

print "Checking for overlap….\n";
print "…this might actually take a while….\n";

$overlapcount=0;
for ($k=1; $k<=$zaehler; $k++) {
$uppercheck=0;
$lowercheck=0;
$progress=($k/$zaehler)*100;
$progress=round ($progress,2);
print STDOUT "$progress % done…\r";
if (substr($atmname_l[$k],0,1) eq "P") {

$res=$resnum_l[$k];
$overlap[$res]=0;

for ($i=1; $i<=$counter; $i++) {

if ($atmname_p[$i] eq "CA") {

$distance=abstand ($x_l[$k]+$translatex_l[$res],$y_l[$k]+$translatey_l[$res],$z_l[$k],$x_p[$i]+$translatex_p,$y_p[$i]+$translatey_p,$z_p[$i]);
if ($distance<=$cutoff) {
$overlap[$res]=1;
if ($z_l[$k] > $middle) {$uppercheck=1;}
if ($z_l[$k] < $middle) {$lowercheck=1;}

}

}

}
$overlapcount=$overlapcount+$overlap[$res];
if ($uppercheck==1) {$upper_rm++;}
if ($lowercheck==1) {$lower_rm++;}

}

}

}
print "\nThere are $overlapcount lipids within cut-off range…\n";
print "$upper_rm will be removed from the upper leaflet…\n";
print "$lower_rm will be removed from the lower leaflet…\n\n";

}

$newlipids=$pcount - $upper_rm - $lower_rm;
$newupper=$uppercount - $upper_rm;
$newlower=$lowercount - $lower_rm;
$totalatmn_new=$totalatmn - ($upper_rm + $lower_rm)*$atomperlipid;

  1. Writing scaled bilayer & centered protein

print STDOUT "Writing scaled bilayer & centered protein…\n";

open(OUTPUT, ">$output");

print OUTPUT "What you read here has nothing to do with anything. So you don't have to read it. Thank you.\n";
print OUTPUT "$totalatmn_new\n";

for ($k=1; $k<=$counter; $k++) {

$newx=$x_p[$k]+$translatex_p;
$newy=$y_p[$k]+$translatey_p;

# print "$newx $newy\n";

printf OUTPUT "%5d%-5s%5s%5d%8.3f%8.3f%8.3f\n",$resnum_p[$k],$resname_p[$k],$atmname_p[$k],$atmnum_p[$k],$newx,$newy,$z_p[$k];

  1. printf OUTPUT "ATOM%7d %4s %-4s%5d %11.3f %7.3f %7.3f %5.2f %5.2f\n",$k,$atmname_p[$k],$resname_p[$k],$resnum_p[$k],$newx,$newy,$z_p[$k],$occupancy_p[$k],$bfactor_p[$k];

}

if ($switch==0) {

for ($k=1; $k<=$zaehler; $k++) {
$res=$resnum_l[$k];
$newx=$x_l[$k]+$translatex_l[$res];
$newy=$y_l[$k]+$translatey_l[$res];

if ($cutoff>0) {
if ($overlap[$res]==0) {

printf OUTPUT "%5d%-5s%5s%5d%8.3f%8.3f%8.3f\n",$resnum_l[$k],$resname_l[$k],$atmname_l[$k],$atmnum_l[$k],$newx,$newy,$z_l[$k];

  1. printf OUTPUT "ATOM%7d %4s %-4s%5d %11.3f %7.3f %7.3f %5.2f %5.2f\n",$k,$atmname_l[$k],$resname_l[$k],$resnum_l[$k],$newx,$newy,$z_l[$k],$occupancy_l[$k],$bfactor_l[$k];

}
}

if ($cutoff==0) {

printf OUTPUT "%5d%-5s%5s%5d%8.3f%8.3f%8.3f\n",$resnum_l[$k],$resname_l[$k],$atmname_l[$k],$atmnum_l[$k],$newx,$newy,$z_l[$k];

  1. printf OUTPUT "ATOM%7d %4s %-4s%5d %11.3f %7.3f %7.3f %5.2f %5.2f\n",$k,$atmname_l[$k],$resname_l[$k],$resnum_l[$k],$newx,$newy,$z_l[$k],$occupancy_l[$k],$bfactor_l[$k];

}

}

}

printf OUTPUT "%10.5f%10.5f%10.5f\n",$box_x,$box_y,$box_z;
close OUTPUT;

  1. Translate protein to Xmin & Ymin = 0

print "\n\nCalculating Area per lipid…\n";

$protein_xmax=int ($protein_xmax+1);
$protein_xmin=int ($protein_xmin);
$protein_ymax=int ($protein_ymax+1);
$protein_ymin=int ($protein_ymin);

$xrange=$protein_xmax-$protein_xmin;
$yrange=$protein_ymax-$protein_ymin;

print "Protein X-min/max: $protein_xmin $protein_xmax\n";
print "Protein Y-min/max: $protein_ymin $protein_ymax\n";
print "X-range: $xrange A Y-range: $yrange A\n";

if ($protein_xmin != 0 or $protein_xmax != 0){

for ($k=1; $k<=$counter; $k++) {

$x_p[$k]=10*$x_p[$k]-$protein_xmin;
$y_p[$k]=10*$y_p[$k]-$protein_ymin;

}
}

  1. Building 2D grid on protein coordinates

print "Building $xrange X $yrange 2D grid on protein coordinates…\n";

#for ($x=0; $x<=$xrange; $x=$x+$gridsize) {

  1. for ($y=0; $y<=$yrange; $y=$y+$gridsize) {

for ($x=0; $x<=$xrange/$gridsize; $x=$x+1) {
for ($y=0; $y<=$yrange/$gridsize; $y=$y+1) {
$grid[$x][$y]=0;
}
}

  1. Calculating area occupied by protein

print "Calculating area occupied by protein..\n";

print "full TMD..\n";

for ($k=1; $k<=$counter; $k++) {
if ($z_p[$k]>=$lower and $z_p[$k]<=$upper) {
$x = int( $x_p[$k] / $gridsize);
$y = int( $y_p[$k] / $gridsize);
$grid[$x][$y]=1;
}
$progress=$k/$counter *100;
$progress=round ($progress,1);
print "$progress % done…\r";
}

$howmany=0;

for ($x=0; $x<=$xrange/$gridsize; $x=$x+1) {
for ($y=0; $y<=$yrange/$gridsize; $y=$y+1) {

$howmany=$howmany+$grid[$x][$y];

}
}

$areaprotein_total=($gridsize)**2 *$howmany *0.01;

$arealipid_total=($box_x * $box_y - $areaprotein_total)/($newlipids*0.5);

print "upper TMD..\n";

for ($x=0; $x<=$xrange/$gridsize; $x=$x+1) {
for ($y=0; $y<=$yrange/$gridsize; $y=$y+1) {
$grid[$x][$y]=0;
}
}

for ($k=1; $k<=$counter; $k++) {
if ($z_p[$k]>=$middle and $z_p[$k]<=$upper) {
$x = int( $x_p[$k] / $gridsize);
$y = int( $y_p[$k] / $gridsize);
$grid[$x][$y]=1;
}
$progress=$k/$counter *100;
$progress=round ($progress,1);
print "$progress % done…\r";
}

$howmany=0;

for ($x=0; $x<=$xrange/$gridsize; $x=$x+1) {
for ($y=0; $y<=$yrange/$gridsize; $y=$y+1) {

$howmany=$howmany+$grid[$x][$y];

}
}

$areaprotein_upper=($gridsize)**2 *$howmany *0.01;

$arealipid_upper=($box_x * $box_y - $areaprotein_upper)/($newupper);

print "lower TMD..\n";

for ($x=0; $x<=$xrange/$gridsize; $x=$x+1) {
for ($y=0; $y<=$yrange/$gridsize; $y=$y+1) {
$grid[$x][$y]=0;
}
}

for ($k=1; $k<=$counter; $k++) {
if ($z_p[$k]>=$lower and $z_p[$k]<=$middle) {
$x = int( $x_p[$k] / $gridsize);
$y = int( $y_p[$k] / $gridsize);
$grid[$x][$y]=1;
}
$progress=$k/$counter *100;
$progress=round ($progress,1);
print "$progress % done…\r";
}

$howmany=0;

for ($x=0; $x<=$xrange/$gridsize; $x=$x+1) {
for ($y=0; $y<=$yrange/$gridsize; $y=$y+1) {

$howmany=$howmany+$grid[$x][$y];

}
}

$areaprotein_lower=($gridsize)**2 *$howmany *0.01;

$arealipid_lower=($box_x * $box_y - $areaprotein_lower)/($newlower);

print "Area per protein: $areaprotein_total nm^2\n";
print "Area per lipid: $arealipid_total nm^2\n\n";

print "Area per protein, upper half: $areaprotein_upper nm^2\n";
print "Area per lipid, upper leaflet : $arealipid_upper nm^2\n\n";

print "Area per protein, lower half: $areaprotein_lower nm^2\n";
print "Area per lipid, lower leaflet : $arealipid_lower nm^2\n\n";

print STDOUT "Writing Area per lipid…\n";

open(OUTPUT, ">$area");

  1. Uncomment this section if you want a plot of the protein area
  1. for ($x=0; $x<=$xrange/$gridsize; $x=$x+1) {
  2. for ($y=0; $y<=$yrange/$gridsize; $y=$y+1) {
  3. if ($grid[$x][$y]==1) {
  4. $xtmp = $gridsize*$x +0.5*$gridsize;
  5. $ytmp = $gridsize*$y +0.5*$gridsize;
  6. print OUTPUT "$xtmp $ytmp\n";}

#if ($grid[$x][$y]==1) { print OUTPUT "$x $y\n";}

  1. }
  2. }

print OUTPUT "$arealipid_total $arealipid_upper $arealipid_lower \n";

close OUTPUT;

print "Done!\n\n\n";

by Shivani Gup[ta (guest), 07 Aug 2017 06:06
AndreaMinoiaAndreaMinoia 02 Jun 2017 18:51
in discussion Hidden / Per page discussions » TINKER explained

Hello. I am sorry I cannot help you. As you can see, this site is not being updated since long time. With all my good will, I had no time to maintain the wiki up to date. Many softwares have evolved in the meantime, and Tinker is no exception. The info on this site are valid for versions 4.x and, to some extent, versions 5.x.

I stop using tinker since version 5.x so I don't know if what I wrote still apply or not, nor I know version 8.

You can either write to Jay Ponder or check the official wiki (web address was in the Tinker website).
Good luck

Andrea

by AndreaMinoiaAndreaMinoia, 02 Jun 2017 18:51
Cole Greenwalt (guest) 02 Jun 2017 17:24
in discussion Hidden / Per page discussions » TINKER explained

Would you shoot me an email? I am trying to set it up in windows and I am actually having more trouble there than I did on Linux ude.yku.g|222rgcz#ude.yku.g|222rgcz I was hoping to find someone else still using this program that is active on boards to get some help. it would be greatly appreciated (:

by Cole Greenwalt (guest), 02 Jun 2017 17:24
Cole Greenwalt (guest) 02 Jun 2017 17:21
in discussion Hidden / Per page discussions » TINKER explained

I am having the same problems using the Linux setup for this.

by Cole Greenwalt (guest), 02 Jun 2017 17:21
shanthi (guest) 01 Jun 2017 04:37
in discussion Hidden / Per page discussions » TINKER explained

Hello all, I have just started to work with tinker software in windows environment. I am trying to convert my internal coordinates/cartesian coordinates to tinker format.I am getting an response "getkey — keyfile specified on command line not found". I just did the example shown in chembyte(ethane).I am getting the same response as well for that.Can someone help me in kicking off this.Any related link in addition will also be appreciated. Thanks in advance :-)

by shanthi (guest), 01 Jun 2017 04:37
Cole Greenwalt (guest) 20 May 2017 01:50
in discussion Hidden / Per page discussions » TINKER explained

Hello all,

I have recently installed TINKER and the Linux executables for TINKER 8 and every time I enter the cartesian coordinate files when prompted for them I am asked for the file again. I am not asked for the parameter file like the tutorial says I should be. Could this be an error with the download or with how I entered the file into my path using the shell. Thanks in advance for assistance.

Cole

by Cole Greenwalt (guest), 20 May 2017 01:50
gao (guest) 08 Nov 2016 10:06
in discussion Hidden / Per page discussions » Accelrys Materials Studio

Sir:

I have a problem when use the Script, it will prompt "Cannot operate upon infinite SymmetrySystem (function/property "Atoms" at -e line 42". I don't find the answer.

by gao (guest), 08 Nov 2016 10:06
Rashid (guest) 21 Apr 2016 17:14
in discussion Hidden / Per page discussions » Analyze and Optimize a peptide with TINKER

Hi I'm trying to predict a small protein structure through minimization and MD. However, I'm having problems with building it as it has disulfide bonds. Protein.exe seems to take in a certain code to input disulfide bonds, and I can't figure it out. Do you guys know how it is? Btw, your tutorial has been a great help to me.

Thanks!

by Rashid (guest), 21 Apr 2016 17:14

Great, Thanks for sharing your creation.

by allwordseoallwordseo, 11 Jan 2015 10:13
Smitha950 (guest) 18 Dec 2014 09:30
in discussion Hidden / Per page discussions » Accelrys Materials Studio

Hey very cool blog!! Guy.. Beautiful.. Wonderful.. I will bookmark your website and take the feeds additionallyKI am satisfied to search out numerous useful information right here in the publish, we want develop more techniques on this regard, thank you for sharing aeaccffebkekckgf

by Smitha950 (guest), 18 Dec 2014 09:30
daria (guest) 18 Dec 2014 09:08
in discussion Hidden / Per page discussions » TINKER explained

Hello all,
Does anyone know which are the units of the Cartesian coordinates and velocity in the file.dyn e.g Amstrong or atomic units?

Thank you

Daria

by daria (guest), 18 Dec 2014 09:08
hyunsung choi (guest) 24 Sep 2014 15:48
in discussion Hidden / Per page discussions » Buildcstruct

I'm just curious why it doesn't give me a exact *.gro file. I tried to use this code " python buildCstruct -s armcnt -g 20 80 arm20x80.gro"
but vmd couldn't recognize what it is. VMD only could figure out one atom. And also I tried " python buildCstruct -s armcnt -g 20 80 arm20x80.xyz"
and tried to convert the xyz-coordinate file into the *.gro file by using "editconf -f arm20x80.xyz -o arm20x80.gro", but the window only shows that
the result of builtCstruct is irregular file to use for GROMACS. I don't know why I wasn't able to get the exact file just like you showed us.
Do you think you could let me know about that?

by hyunsung choi (guest), 24 Sep 2014 15:48
ghadafi (guest) 20 May 2014 15:15
in discussion Hidden / Per page discussions » Buildcstruct

Please Give the pdb file guys….

by ghadafi (guest), 20 May 2014 15:15

Hello All,

Like Pablo, I am also interested in calculation solvation free energies using tinker. I have worked with tinker and amoeba before to do some MD simulations, but I am not able to prepare correct input for calculating the free energy.
There is a example for the mutation of Chloride to bromide in the tinker examples.
How will the input file look like if I want to calculate the free energy of solvation of only Chloride ion in waters?

It would be great if someone gives good example of doing that using tinker.

Thank you in advance.
Best regards.

Pablo (guest) 02 Dec 2013 14:42
in discussion Hidden / Per page discussions » TINKER explained

Hello, well, I am interested in solvation free energies, and I was told to use TINKER and AMOEBA. However, today I recently downloaded TINKER and it seems to have a lot of information and programs at once.

I wonder if someone can help me, how do I use TINKER and AMOEBA in order to calculate solvation free energies?

Thank you for your time,
Regards

by Pablo (guest), 02 Dec 2013 14:42

Hi Guido, if parameters per Na+ are available in the force field you use, or you can add them, there is no problem to add counter ions to your rna. It may be necessary, though, to fix their position in space (keyword inactive), but I will try before leaving them free, at least for the minimization. Of course, you have to introduce them in the proper position along your rna ;)
Andrea

by AndreaMinoiaAndreaMinoia, 15 Aug 2013 09:22
Guido (guest) 02 Aug 2013 16:38
in discussion Hidden / Per page discussions » Analyze and Optimize a peptide with TINKER

according to your experience is it possible to add Na+ ions to a structure before minimization?
I'm purposing to minimize some rna 3d structures in vacuo and I'd like to add Na+ counter ions to minimize the effects of negative phosphate groups.
Thank you for your tutorial they are very useful and interesting
best
Guido

by Guido (guest), 02 Aug 2013 16:38
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