[gmx-users] pdb2gmx : treat CL as C
tsjerkw at gmail.com
Tue Nov 17 15:47:16 CET 2009
Oops, there's an .rtp entry. Shame on me :$
Maybe a good idea though to post the output of pdb2gmx.
On Tue, Nov 17, 2009 at 3:44 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>> What is the problem? It looks like you got everything to work, but the .pdb
>> file you've posted is misformatted on the CL lines:
>> ATOM 14 C14 PCD 1 -2.372 -1.395 0.000 1.00 0.00
>> ATOM 15 CL1 PCD 1 5.070 1.618 -0.001 1.00 0.00
>> Note how the atom name "CL1" is shifted relative to "C14" so pdb2gmx handled
>> it incorrectly. Formatting is not merely a suggestion!
> This is correct formatting, according to the PDB file format! Of the
> four character positions denoting the atom name, the first two are
> used to indicate the element.
> But what is this talking about pdb2gmx if there's a hand written
> .top/.itp file in stead of an .rtp entry? Of course it will fail. And
> if that's not the problem, Nilesh is still not providing a proper
> description of what he's doing.
> Tsjerk A. Wassenaar, Ph.D.
> Computational Chemist
> Medicinal Chemist
Tsjerk A. Wassenaar, Ph.D.
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