[gmx-users] question about pdb2gmx

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

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?

Best,
 Eva

>
>
> On 7/19/12 5:00 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I want to add protonation states to my protein with pdb2gmx.
>> I now that there are the options:
>>
>> -lys -arg -asp -glu -his
>>
>> to do this.
>>
>> But was is about the cystein. How can I protonate this one?
>> Is there also an option for it which I haven't seen?
>>
>
> The -ss flag controls cysteine protonation, in the sense that you can
> toggle
> between disulfide and free forms of cysteine.  Some force fields include
> an
> anionic form of cysteine as well.
>
> -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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