AMBER Archive (2009)

Subject: RE: [AMBER] "Could not find bond parameter"

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jan 23 2009 - 12:29:46 CST

Dear George,

> I am experiencing the following problem when trying to save the parameter
> file of my protein.
>
> <saveamberparm> generates the following output:
>
> 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
> etc.
>
> I'm dealing with a small protein with 3 disulfide bonds.
>
> I'm using leaprc.ff99SB as a forcefield

Cysteines involved in disulphide bonds have to be renamed CYX in the pdb.

A CYS residue has types CT-SH-HS

while CYX has CT-S

So not only do you have additional hydrogens here that shouldn't be there
the types are incorrect for disulphide bonds. Edit your pdb and reload if
and all should be good.

All the best
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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