AMBER Archive (2004)

Subject: RE: AMBER: generating parmfile containing topology and parameter information

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Nov 22 2004 - 15:46:30 CST

Dear Nitin,

> 1) How can I create the parm file containing the topology and
> parameter information for PIP2?

See the amber tutorials - I have written one which explains how to use xleap
to create a prmtop and inpcrd file for a system containing non-standard
residues - you can modify this.

http://amber.scripps.edu/tutorial/

> 2) I have the pdb file only for the lipid "POPC" and I have the other
> informattion (parameters and topology) in 'charmm' format.
> Can I change
> the charmm file into an appropriate (properly scaled) 'amber'
> file format?

Not easily (although somebody correct me if I am wrong here) as far as I
know there is no automated way to do this. However, the charmm and amber
force fields are sufficiently similar that you should be able to get a
listing of the parameters for your system (atom types, bonds angle dihedrals
etc) from the charmm topology file. You can then create yourself an amber
frcmod file from this that you can load into xleap when creating the amber
topology file.

You should ideally calculate the charges using Amber's RESP method rather
than using the charges from the charmm topology file - see the amber website
for info on this.

> Is there an amber topology and parameter file for this lipid
> 'POPC' or any other lipid?

There may be - try google and see if you get anything...

> I am a complete novice in this regard so I would be very
> thankful if the reply could be a detailed one.

Go through the Amber Workshop tutorials and things will become a lot
clearer.

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_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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