[gmx-users] protonated cys -S
mgoette at mpi-bpc.mpg.de
Fri Nov 10 13:41:21 CET 2006
Try renaming the Cys in the the PDB to CYS2.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Giacomo Bastianelli wrote:
> Hi Tsjerk,
> the distance of the "not formed" S-S is 0.202
> while the two "formed" S-S are 0.204 and 0.203.
> Therefore, gromacs should recognize all three and
> create the SS bonds.
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> this is the second line of my specbond.dat
> Tsjerk Wassenaar wrote:
>> Hi Giacomo,
>> The two sulphur atoms have to be at a proper distance to be recognized
>> as involved in a S-S bond. In your case, if you're certain that there
>> should be a bond, you have to edit the file specbond.dat, find the
>> entry which links two cysteine residues and set the distance to the
>> actual distance in your structure (there is a 10% margin).
>> Hope it helps,
>> On 11/10/06, Giacomo Bastianelli <gbastian at pasteur.fr> wrote:
>>> Dear users,
>>> I have just found that gromacs protonate the -S of
>>> my Cys and I would like to have it deprotonated
>>> to form a disulphide bond (It is present in the original
>>> pdb file).
>>> Is there any way I can modify it?
>>> thanks in advance,
>>> gmx-users mailing list gmx-users at gromacs.org
>>> 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/mailing_lists/users.php
> gmx-users mailing list gmx-users at gromacs.org
> 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/mailing_lists/users.php
More information about the gromacs.org_gmx-users