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Hello, Rose:
Thank you very kindly for your helps. Now I understand what is going on.
Thank you for your response on my MD post. I am still reading your
comments. Will write you later.
Best regards.
Bo Yang
On Fri, 9 Jul 2004 11:27:13 -0700 "Ross Walker" wrote:
> 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
> >
> >
> >
> > --------------------------------------------------------------
> > ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
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Received on Fri Jul 09 2004 - 19:53:01 PDT
