AMBER Archive (2004)

Subject: RE: AMBER: frcmod_dmso

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Oct 01 2004 - 17:05:05 CDT

Dear Vincent,

> ;;;;;;;;;
> Loading parameters: /usr/local/amber8/dat/leap/parm/frcmod.dmso
> Reading force field mod type file (frcmod)
> solvateBox: Argument #2 is type String must be of type: [unit]
> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]

Have you cut the output up here? I can't see how the colvateBox error comes
immediately after the reading force field mod message. Are you sourcing all
of the commands from a leap script file you created? Or are you typing them
interactively into leap?

Either way we need to see all of the commands you have entered into leap so
that we can see where the error is. Also, have you created a separate DMSO
unit? Just loading the modified parameters won't help you if you don't have
a DMSO unit defined in xleap.

You will need to create a unit called DMSO with the connectivity and atom
types:

      O
      |
      S
     / \
H1-CT CT-H1
   /\ / \
 H1 H1 H1 H1

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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