[gmx-users] more than one protonation per residue with pdb2gmx

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

I have another question about the option -ter of the pdb2gmx command.

I choose it because I thought that this is a way that I can determine what
shell happen with the termini but I was not ask anything by the program.

My aim is it to block the termini with a neutral group. Is there a way to
do this with gromacs?

Best,
Eva

> Hi Justin,
> thank you for your mail.
> Sorry that I didn't first check than help.
> Eva
>
>>
>>
>> On 7/11/12 10:24 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>> Hi everybody,
>>>
>>> I wanted to ask if there is a possibility to tell pdb2gmx which
>>> residues
>>> I
>>> want to be protonated or not.
>>> So that I can for example say HIS at position 29 shell be protonated
>>> twice.
>>>
>>> I need this for further electrostatic analysis.
>>>
>>
>> Please read pdb2gmx -h.  There are tons of available options to control
>> protonation of any and all titratable residues.
>>
>> -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
>>
>> ========================================
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Only plain text messages are allowed!
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>