[gmx-users] problem in simulation mutant p53 protein both in swiss pdb viewer and energy minimization with gromacs

[Justin Lemkul]

On 4/6/14, 7:05 AM, delara aghaie wrote:
> Dear Gromacs Users
> I want to simulate human p53 protein and two of its mutants to see how mutation affect its structural properties.
> I obtained the nature and mutant pdb files form protein data bank.
> when I submitted the mutant files to pdb2gmx command it gave error on misiing atoms. I fixed the pdb files using swiss pdb viewer.
> There is an optin in this program which minimizes the energy of pdb file, but when I wanted to minimize the energy of mutant pdb file, I got error. You can see the error in attached files. (I hhave attached the image of error page)
>
> After seeing this error, I decided to ignore this stage and submit the mutant pdb file, taken from swiss pdb viewer to pdb2gmx command. When I did that, I did not get error and decided to acceot the energy minimization using gromacs instead of the swiss pdb viewer.
> Now the questions:
>
> 1) how can I fix the error by swiss pdb viewer?
> 2) Is it right to take pdb file with out energy minimizing from swiss pdb viewer and submit it for simulation to gromacs?

Gromacs can do minimization; there is no need to pre-minimize the structure 
before doing anything in Gromacs.

> -------------
> The nest problem is that when I submitted the mutant pdb file taken from swiss pdb to pdb2gmx and it worked successfully, then I made the simulation box and added the required ions according to hustin lyzozyme tutorial.
> When I did energy minimization I got strange output files besides the regular ones:
> the name of those files are:
> step14b_n0.pdb
> step14c_n0.pdb
> step15b_n4.pdb
> step15c_n4.pdb
>
> ....
> It would be greatly appreciated if you let me know what are these files and what I should do about them?
> can I continue the simulation by just ignoring them?
>

The step*.pdb files indicate instability, information about which is also 
printed in the .log file.  You have bad contacts somewhere that EM has problems 
resolving.  If the EM finished successfully, it's probably not a big deal and is 
just an indicator of bad starting geometry (probably your mutated residues 
cannot be accommodated by the crystal structure, indicating there will be 
changes later on).  If, however, the local structure in the locations where the 
bad contacts occurred (again, see the .log file for the problematic atoms) 
became distorted as a result, then you have a problem that needs to be dealt 
with (i.e., you probably need a different starting structure).

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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