RE: AMBER: frcmod_dmso

From: Ross Walker <>
Date: Tue, 5 Oct 2004 13:10:41 -0700

Dear Vincent,

> >>rosource leaprc.ff03
> loadAmberParams frcmod.dmso
> metenk = sequence {NTYR GLY GLY PHE CMET}
> solvateBox metenk DMSO 10.0 0.8

The problem is here. The frcmod.dmso file simply provides the parameters for
DMSO, it does not provide any connectivity/topology information for DMSO.
For this you will need to create a new unit called DMSO in xleap that has
atom types that match those in the frcmod.dmso file. You can save this unit
as a lib file for later use.

Saveoff DMSO dmso.lib

Then you should be able to use solvate box to solvate your system in DMSO.
After the solvate command use "edit metenk" in xleap to see if you have what
you want. Visualising your system before running simulations is always a
good idea.

> saveamberparm metenk metenk.crd

> The eg on page 29 (for MEOH) worked fine for my peptide- I was able to
> generate the crd and top files, and even minimised the whole system
> (using sander 8).

This is because MEOH is defined as a unit in xleap and so xleap knows about
it's topology. Type 'list' in xleap to get a list of units the program knows

> However, in the case of DMSO, whilst I was able to generate
> the crd and
> the top files, my problem was with the minimisation.

What you have probably got is your system without any solvent around it. Try
using ambpdb to generate a pdb from the prmtop and crd files and then
visualise this pdb inn something like VMD. The problem should then be

> was running, my tmp.out files were empty.-and therefore
> attributed this to my leap files.

Yes, you are probably trying to run periodic boundaries on a system that
contains no solvent...

So, create the DMSO unit with the correct atom types. Save it as dmso.lib.

Then load the frcmod.dmso file.
Then load your system.
Then solvate
Then edit and check that it looks good.
Then save the prmtop and crd files
Then convert to pdb and double check that it still looks good.
Then run your minimisation.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Tue Oct 05 2004 - 21:53:00 PDT
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