On Fri, Sep 06, 2013, Krati Sharma wrote:
>
> I am generating the solvent file using command
> ambpdb -aatm -p protein.top <protein_min.crd> protein_solvent.pdb
>
> When the protein is lengthy, its causing format problem during tleap run.
>
> If you see below the chain is ending at 2163 and the chain b is starting
> from 2164 instead of 1.
This is expected: the prmtop file that ambpdb is using numbers residues
sequentially, not starting over again for each chain.
>
> ATOM 34303 C ARG 2163 5.387 47.227 -15.222 1.00
> ATOM 34304 O ARG 2163 5.611 47.786 -14.144 1.00
> ATOM 34305 OXT ARG 2163 5.440 47.901 -16.248 1.00
> TER
> ATOM 34306 N THR 2164 -15.132 51.856 34.718 1.00
> ATOM 34307 H1 THR 2164 -14.494 51.092 34.890 1.00
> ATOM 34308 H2 THR 2164 -15.462 51.795 33.765 1.00
>
> This cause error on running tlesp.If I reduce gap between ATOM and the
> number 34303, tleap is reading full residue ARG otherwise it reads RG and
> causing fatal error.
I guess I can't see the problem: the "ARG" string for atom 34303 appears
in columns 18-20, as it should. Can you give the exact error message from
tleap? Can you be more specific about exactly what you did to "reduce the
gap" between ATOM and the number? (what did the line originally look like?
what did you change?)
Is the result any better if you leave out the -aatm flag? You may be the only
person who has used that option in years: it no longer is very useful
now that the PDB has gone to the version 3 atom naming scheme. There could be
some sort of bug with that flag.
...dac
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Received on Fri Sep 06 2013 - 05:30:02 PDT
