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
<jalem...@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 <jalem...@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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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