[gmx-users] energy minimization

farial tavakoli farial.tavakoli at ymail.com
Sun Feb 25 11:46:39 CET 2018

Dear Justin
In according to obtaining positive binding free energy using g_mmpbsa for my complex which has 2 phosphotyrosine residues and is simulated by charmm36 force field , I sent an email to g_mmpbsa mailing list and informed them to help me for solving my problem, but they replied me : " we have not tested the g_mmpbsa with charmm36 so we can't say about the validity. Other members of g_mmpbsa tool, also previously reported about the positive binding energy when using charmm36 force field." I sent another email to them :would you please advice me how could I calculate the  free binding energy of my complex (receptor and ligand that has 2 phosphotyrosine residues ) which has been simulated by charmm36 all atom force field? but I have not any response yet.
 so I decided to use a modified amber99s force field to use in gromacs to simulate my complex. and then use g_mmpbsa to calculate the binding energy. I searched the net and found this one to modify the amber99s ff : http://www.pharmacy.manchester.ac.uk/bryce/amberbut it is not for gromacs. Would you please advice me how can I get a modified amber force field to simulate my complex using gromacs?or help me how  can I calcualte the binding energy of my complex which is simulated by charmm36 in gromacs?
with best regardsFarial

    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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