[gmx-users] energy minimization

Justin Lemkul jalemkul at vt.edu
Sat Jul 14 16:05:09 CEST 2018

On 7/14/18 5:03 AM, farial tavakoli wrote:
> 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?

"No such file or directory" means the file isn't in the working 
directory. This is a generic error message from your shell and nothing 
specific about the script itself.

> Farial
> best
>      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.
> -Justin
>> 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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