[gmx-users] question about pdb2gmx

[reisingere at rostlab.informatik.tu-muenchen.de]

There is only one Cystein:


ATOM   1797  N   CYS A 211      10.568   1.888   4.891  1.00  1.00
ATOM   1798  CA  CYS A 211      11.782   1.312   5.391  1.00  1.00
ATOM   1799  CB  CYS A 211      12.968   1.606   4.452  1.00  1.00
ATOM   1800  SG  CYS A 211      14.599   1.282   5.172  1.00  1.00
ATOM   1801  C   CYS A 211      12.106   1.904   6.723  1.00  1.00
ATOM   1802  O   CYS A 211      12.427   1.169   7.655  1.00  1.00

Eva

>
>
> On 7/19/12 6:17 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi Justin,
>> thank you for your answer.
>> I already tried the -ss command but nothing happens. The program just
>> writes the topology file but it does not ask me anything. My command
>> was:
>>
>> pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3m71.top -ss -water tip3p -ff
>> amber03
>>
>> is there something wrong with this command?
>
> No, it's fine.  How many cysteines are in the structure?
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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