[gmx-users] pdb2gmx : treat CL as C

[Tsjerk Wassenaar]

Oops, there's an .rtp entry. Shame on me :$
Maybe a good idea though to post the output of pdb2gmx.

Cheers,

Tsjerk

On Tue, Nov 17, 2009 at 3:44 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Justin,
>
>> 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
>> C
>> ATOM     15 CL1  PCD     1       5.070   1.618  -0.001  1.00  0.00
>>  CL
>>
>> 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
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist