[gmx-users] Query on g_mmpbsa in gromacs

[Justin Lemkul]

On 3/29/16 1:25 AM, Prasanna Dr wrote:
> Hi,
> Thanks for your quick response.
>
> AMBER mmpbsa does amino-acid pairwise residue decomposition. Pairwise
> decomposition energy is very suitable input for weighted network analysis
> (to understand the information flow between residues and to find key
> amino-acids of a functional protein). I tried to convert gromacs parameters
> into AMBER parameters, but I couldn't get success as  I am using modified
> force field in gromacs. So values of pairwise residue decomposition is
> important for further analysis (Reference:
> http://pubs.acs.org/doi/abs/10.1021/acs.biochem.5b00946). I want do similar
> kind of analysis as of reference article using g_mmpbsa (rashmikumari and
> group) of gromacs.
>

There is a help forum for g_mmpbsa that may be more suitable for this question 
(as g_mmpbsa is not an official GROMACS program):

https://groups.google.com/forum/#!forum/g_mmpbsa

-Justin

>
> Hi,
>
> Probably you can find a way to compute a number with this non-GROMACS tool.
> But is there any evidence to support that such a number will mean anything?
> MM force fields are pairwise additive, not decomposable.
>
> Mark
>
> On Mon, 28 Mar 2016 14:37 Prasanna Dr <adveirprasanna at gmail.com> wrote:
>
>> Hi
>>
>> I have been using g_mmpbsa of Rashhmi Kumari and group to calculate
> binding
>> energy of lipids in protein-lipid complex. I got a quite good results with
>> g_mmpbsa. Now, In my next step I need to perform network analysis where
>> pairwise interaction energy from mmpbsa will be considered.
>>
>> I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
>> generated residue decomposition energy of aminoacids with lipid (not
>> between aminoacids) as shown below  (for example purpose)
>>
>> 1            1.0784
>> 2            -0.0261
>> 3            0.9493
>> 4            0.0206
>> 5            -0.0583
>> 6            0.0061
>> 7            -0.0278
>> .
>> .
>> .
>> 450
>>
>> While running mmpbsa my first input was protein and second input was lipid
>> (in place of ligand). Now I have interaction energy of each aminoacid with
>> lipid .
>>
>> Now,  I need interaction energy between aminoacids. like 1st aminoacid
> with
>> remaining 499  aminoacid and 2nd with remaining 449 aminoacids and so on.
>>
>> Is it possible to calculate interaction energy between amnoacids and with
>> lipids using g_mmpbsa (n X n matrix of energy values) ?
>>
>> --
>> D R Prasanna

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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