[gmx-users] pdb2gmx : treat CL as C

[Nilesh Dhumal]

Tsjerk,

When I open di.pdb (output file) in VMD. I see all CL are repalced by C.
I can't go to next step. What information do you want more.  I checked the
format of pdb file again. Its looks dioxin.pdb is ok. After running
pdb2gmx, the di.pdb output file don't have any CL atom. Hopes you get me
now
Nilesh

On Tue, November 17, 2009 9:44 am, Tsjerk Wassenaar 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
> --
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