Re: [AMBER] Issue with running sander with SHAKE

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Tue, 29 Nov 2011 23:52:05 +0400

Dear David, I've got a simple solution from Yue Yang from MCBP team.
When I place zinc atom right after the protein, not after the ligand there is no such issue. In general I didn't thought it may make a difference as far as TER records are ok, but it looks like the order in which zinc and ligand records are mutually placed makes difference.
So now that problem looks solved. Probably it is some common issue about mutual order of metals bound to proteins and other non-metal HETATM records.

Best regards,
Andrew

29.11.2011, 18:42, "David A Case" <case.biomaps.rutgers.edu>:
> On Sat, Nov 26, 2011, Andrew Voronkov wrote:
>
>> šI have found indication of problem, but have no idea how to solve it.
>> šIn PDB file created from inpcrd and prmtop there is one RES atom from ligand in protein:
>>
>> šATOM šš3308 šO ššGLU šš210 ššššš58.563 š30.137 š20.807 š1.00 š0.00 ššššššššššO
>> šATOM šš3309 šOXT GLU šš210 ššššš59.202 š29.891 š18.732 š1.00 š0.00 ššššššššššO
>> šATOM šš3310 šC6 šRES šš211 ššššš47.114 š26.505 š42.295 š1.00 š0.00 ššššššššššC
>> šTER
>> šATOM šš3311 šH5 šRES šš211 ššššš46.856 š26.607 š43.346 š1.00 š0.00 ššššššššššH
>> šATOM šš3312 šC4 šRES šš211 ššššš47.882 š25.415 š41.887 š1.00 š0.00 ššššššššššC
>> šATOM šš3313 šH3 šRES šš211 ššššš48.209 š24.689 š42.629 š1.00 š0.00 ššššššššššH
>>
>> šbut this was not the case in original PDB, so I have no idea why it has migrated.
>
> A similar problem came up recently, and I think it is related to exactly how
> the prmtop is created, and perhaps to the presence of cross-links between
> protein chains.
>
> Can you post the exact tleap commands and procedure you used to create the
> prmtop file? šWe need to be able to reproduce the problem in order to debug
> it.
>
> As a workaround, šyou can try to edit the ATOMS_PER_MOLECULE section in the
> prmtop file. šIt is likely that the entries there are wrong, and you should
> enter the correct number of atoms for each "molecule" (group of atoms that are
> connected by bonds), in the order they appear in the prmtop file. šIf all the
> atoms in a single molecule are not together in the order they appear in the
> input pdb file (or in the prmtop file) that may be the origin of the problem.
>
> ....thanks...dave case
>
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Received on Tue Nov 29 2011 - 12:00:05 PST
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