Try renaming the Cys in the the PDB to CYS2.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.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
Thanks,
Giacomo
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,
Tsjerk
On 11/10/06, Giacomo Bastianelli <[EMAIL PROTECTED]> 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,
Giacomo
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