[gmx-users] energy minimization

farial tavakoli farial.tavakoli at ymail.com
Sat Jul 14 11:03:16 CEST 2018

Dear justin

I am trying to run a simulation on my complex which has small molecule as a ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on linux. then typed "perl -v" to check if it is installed. the perl 5.20.1 was installed. 
but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type itp/top] " command to generate ligand topology , faced with this error:
Can't open perl script "topolgen.pl": No such file or directory
Infact I am new user in generation topology for small molecules using OPLSAA ff. Would you please  help me to figure out this problem? 

    On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul <jalemkul at vt.edu> wrote:  

On 2/20/18 12:52 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear Justin
> Thank you for the reply
> You meant , to tweak the emtol doesn't have noticable affects on the conformational enssemble generated by MD?

Precisely what I said, yes.


> Sent from Yahoo Mail for iPhone
> On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 2/20/18 4:52 AM, farial tavakoli wrote:
>> Dear GMX users
>> I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, respectively. While, I calculated binding energy before for many other complexes without any phosphate groups using OPLS all atom force field and pdie = 2 and obtained minus energy. But this time , I dont know why I got positive binding energy? Is it because of charmm36 all atom force field , the phosphate groups or it is needed to be energy minimized under more restriction situations?
>> I am checking different factors to understand its reason, so I wanted to know , would it be ok if I energy minimize the complex with more restriction situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? I think the positive binding energy might be because of the complex didnt minimized well. however I checked the em.log file and saw it was minimized well:
>> Steepest Descents converged to Fmax < 1000 in 241 steps
>> Potential Energy  = -6.5047744e+05
>> Maximum force     =  9.8285083e+02 on atom 3335
>> Norm of force     =  3.6905827e+01
>> Is there anyone can advice me in energy minimization with emtol 800?
> The purpose of energy minimization is to establish a reasonable starting
> point for your simulation. Tweaks to emtol will have little to no
> noticeable bearing on the conformational ensemble generated by MD.
> -Justin


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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