Russell Green wrote:
I did try changing the bond length but it wouldn't catch all the
disulfides. I do have multiple chains but I don't believe they should be
merged. My current work around is to just leave the disulfide residues
named CYX according to the amber format and then change them to CYS2 in
the .itp files for the corresponding .top file. This way pdb2gmx doesn't
protonate the disulfide residues and the charges for CYS2 are
maintained. If anyone thinks this is not a good idea, please tell me.
it's still not clear what you want to do. if your CYS are at 0.2 nm
distance pdb2gmx will make the bonds. if they are not, why would you
want them to form? anyway, if you want to do that, please follow
Tsjerk's advice below.
Thanks,
Russell
On 7/2/07, *Tsjerk Wassenaar* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Hi Russel,
You never mentioned the distance between the
'sulphurs-that-wouldn't-connect'. Are they beyond the range normal for
disulphide bonds? If so, you could try to add an additional entry in
the specbond.dat file with a different bond length. Maybe you'll have
to change the residue name first, although it could work without (I
don't know whether pdb2gmx properly handles multiple multiple
distances for the same atom pair, but it's easy to find out).
Another thing you never mentioned is whether the cysteines are from
one chain or from different chains. In the latter case, you have to
use the option -merge with pdb2gmx. pdb2gmx will not usually make
bonds between different chains.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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