AMBER Archive (2005)

Subject: RE: AMBER: Problem saving file in xleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Mar 15 2005 - 12:02:32 CST

Dear Atilio,

> I am trying to bind a metal complex to a small DNA seqence
> in xleap, I
> loaded the metal complex as a prepin file and created the Pt-N bond
> with DNA. But when trying to save parameters and input coordinates I
> got the following message:
>
> For atom: .R <<1> 35> .A <Cl 1> could not find type:Cl
> Parameter file was not saved.

See this tutorial->
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/index.htm

This will show you how to add Pt atom types and add the parameters for the
Pt-N bond. As for the error about unfound atom type Cl what force field file
did you load when you ran leap? Do you have a stray chlorine atom in your
pdb file or was this chlorine added by an addions command?

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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