[gmx-users] 答复: membrane protein simulation - errors

[Justin Lemkul]

On 9/18/14 1:51 PM, Yunlong Liu wrote:
> Hi Justin,
>
> I built Gromacs 5.0.1 but it doesn't work even with pdb2gmx. Since my protein is patched with -NH3+ and -COO- at the N-terminus and C-terminus. I used -ter flag.
>
> But the program cannot recognize the terminus and returns error.
>

This probably comes from an ill-constructed coordinate file.  This would 
probably also explain the somewhat cryptic message you got from grompp.

> I switched back to the Gromacs 5.0-rc1. It works fine with pdb2gmx and it fixed the error but got the previous "Non default U-B types" errors.
>
> I don't know what is the U-B types and how it is define in the gromacs.
>

It's because you're processing water, and pdb2gmx builds angles that it 
shouldn't in the TIP3P molecules.  You should be able to strip out the water and 
ions, process the protein and membrane, then add back the water and ion 
coordinates.  Update [molecules] and proceed.

I still would strongly advise against using beta releases for production work. 
A released version of Gromacs with bug fixes is more reliable.

-Justin

> Yunlong
> ________________________________________
> 发件人: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> 代表 Justin Lemkul <jalemkul at vt.edu>
> 发送时间: 2014年9月18日 20:30
> 收件人: gmx-users at gromacs.org
> 主题: Re: [gmx-users] membrane protein simulation - errors
>
> On 9/17/14 6:54 PM, Yunlong Liu wrote:
>> Hi,
>>
>>
>> I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my membrane protein system with POPC membrane and TIP3P water in VMD. Then I used gmx pdb2gmx to build gromacs topology files.
>>
>>
>> My force field is charmm22* and it contains a lipids.rtp entry. It can successfully recognize the POPC molecules in my pdb and the water. But it keeps complaining something like this :
>>
>>
>> Processing chain 7 'L' (5360 atoms, 40 residues)
>> Warning: Starting residue POPC1 in chain not identified as Protein/RNA/DNA.
>> Warning: Starting residue POPC2 in chain not identified as Protein/RNA/DNA.
>> Warning: Starting residue POPC3 in chain not identified as Protein/RNA/DNA.
>> Warning: Starting residue POPC7 in chain not identified as Protein/RNA/DNA.
>> Warning: Starting residue POPC8 in chain not identified as Protein/RNA/DNA.
>> More than 5 unidentified residues at start of chain - disabling further warnings.
>> Problem with chain definition, or missing terminal residues.
>> This chain does not appear to contain a recognized chain molecule.
>> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
>>
>> Then I modified the residuestypes.dat to add POPC and TIP3 into the file but it still keeps complaining.
>>
>> I tried to ignore this and run grompp -f minim.mdp -c my.gro .. to generate the tpr file but I got an error like this:
>>
>> -------------------------------------------------------
>> Program gmx, VERSION 5.0-rc1
>> Source code file: /home/yunlong/Downloads/gromacs-5.0-rc1/src/gromacs/gmxpreprocess/toppush.c, line: 2393
>>
>> Fatal error:
>> Invalid Atomnr j: 5, b2->nr: 3
>>
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------?
>>
>>
>> I am wondering whether I can do membrane protein simulation in Gromacs without building the system in Gromacs.
>>
>
> It's certainly possible, but I'd start with using an actual release version of
> Gromacs, rather than 5.0-rc1.  Try again with 5.0.1.
>
> -Justin
>
> --
> ==================================================
>
> 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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-- 
==================================================

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

==================================================