On Tue, Oct 31, 2017 at 8:12 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Oct 30, 2017, Hai Nguyen wrote:
> >
> > the script does work as expected. The index you saw did not reflect the
> > atom index.
>
> ?? Does this mean there is no problem? Did you send at17.pdb to tleap?
>
uhm, I just tried and seems a problem :D.
WARNING: There is a bond of 3.114709 angstroms between:
------- .R<CYX 4>.A<SG 8> and .R<CYX 148>.A<CB 5>
Removing the CONECT field indeed resolve the case.
> > PS: If you see the at17.pdb content, you can see something like
> >
> > ATOM 2354 N GLN I 298 38.581 11.502 -4.835 1.00 33.77
> N
> > TER 2355 GLN I 298
>
> The ambpdb code (aka cpptraj) slightly violates the PDB practice by not
> incrementing the atom number on a TER card. This is extremely convenient
> since then the atom number in columns 7-11 actually *is* the Amber atom
> number
> (starting from 1).
>
> I'm thinking that pdb4amber should do the same thing. I think (not tested)
> that this would fix the problem, and would make pdb4amber more consistent
> with
> the rest of Amber. (I've not yet seen a case where a code makes use of the
> conents of columns 7-11 on a TER card.)
>
pdb4amber depends on ParmEd and I am not sure if there is an option for
that.
https://github.com/Amber-MD/pdb4amber/blob/master/pdb4amber/pdb4amber.py#L372
Hai
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Received on Tue Oct 31 2017 - 06:00:05 PDT
