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:
>
>> I have found indication of problem, but have no idea how to solve it.
>> In PDB file created from inpcrd and prmtop there is one RES atom from ligand in protein:
>>
>> ATOM 3308 O GLU 210 58.563 30.137 20.807 1.00 0.00 O
>> ATOM 3309 OXT GLU 210 59.202 29.891 18.732 1.00 0.00 O
>> ATOM 3310 C6 RES 211 47.114 26.505 42.295 1.00 0.00 C
>> TER
>> ATOM 3311 H5 RES 211 46.856 26.607 43.346 1.00 0.00 H
>> ATOM 3312 C4 RES 211 47.882 25.415 41.887 1.00 0.00 C
>> ATOM 3313 H3 RES 211 48.209 24.689 42.629 1.00 0.00 H
>>
>> but 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? We need to be able to reproduce the problem in order to debug
> it.
>
> As a workaround, you can try to edit the ATOMS_PER_MOLECULE section in the
> prmtop file. It 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. If 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
