Re: force field parameters for phosphoserine

From: David A. Case <>
Date: Tue, 29 Apr 2003 07:56:48 -0700

On Tue, Apr 29, 2003, Christoph Kluck wrote:

> I generated prep and parm file of SEP using antechamber, but neverthess
> xleap is complaining when generating the topology file and coordinate file
> for a peptide containing a SEP:
> Could not find bond parameter for: P - O Could not find bond parameter for:
> O - P

Something is wrong here. The above atom types use upper case letters, but
antechamber uses lower case letters for atom types. The prep file you
sent had lower case atom types....How did you create the file "SEP.lib"?

> Did I miss some steps in xleap?
> (the commands I did:
> loadamberparams parm94.dat

you don't need the above; replace it with "loadAmberParams gaff.dat"

> loadoff SEP.lib

After this step, you can type "desc SEP.1" to list the atoms in the 1st
residue of SEP, then "desc SEP.1.P" to describe the properties of the
phosphorus atom. It *should* have an atom type of "p5", not "P".

This may help track down what is going on.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Tue Apr 29 2003 - 16:53:01 PDT
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