Dear Bo,
You need to edit your pdb file and change the cysteine residues involved in
the disulphide bond from CYS to CYX before loading into leap. In this way
they won't be hydrogenated and so you can then bond the two sulphur atoms.
You will not then need HS-SH-SH-X parameters.
I hope this helps
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of bybaker.itsa.ucsf.edu
> Sent: 09 July 2004 11:16
> To: amber.scripps.edu
> Subject: AMBER: Disulfide bond command
>
> Hello, Amber:
>
> My question is about how to add bond information about
> disulfide bond. I
> notice that some one post the same question before, but I
> could not found
> the answer for it from Amber mail-relector. So I post the
> question again,
> and hope to get some help.
>
>
> I tried to load my .pdb file with tleap. The file contains
> one disufide
> bond. I use bond command as described in manual:
>
> bond test.100.SG test.261.SG
>
>
> And 'saveAmberParm' but get the following messages:
>
>
>
> > bond test.100.SG test.261.SG
> > saveAmberParm test test.prmtop test.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: SH - SH
> Building angle parameters.
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: SH - SH - CT
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: CT - SH - SH
> Building proper torsion parameters.
> ** No torsion terms for HS-SH-SH-CT
> ** No torsion terms for HS-SH-SH-HS
> ** No torsion terms for CT-SH-SH-CT
> ** No torsion terms for CT-SH-SH-HS
> Building improper torsion parameters.
> total 634 improper torsions applied
> Building H-Bond parameters.
> Parameter file was not saved.
>
>
> Can anyone please let me know how to fix the problem?
>
> Thank you
>
> Bo Yang
>
>
>
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Received on Fri Jul 09 2004 - 19:53:01 PDT
