AMBER Archive (2003)

Subject: AMBER: DMSO box

From: Dalmaris, John (john.dalmaris_at_imperial.ac.uk)
Date: Fri Sep 12 2003 - 04:25:21 CDT

Dear all,

I am trying to solvate a small peptide in a DMSO box. Initially, I developed
the DMSO unit using parameters from J.Phys.Chem. B, (1998), 102, 8070-8079
and constructing a 3D DMSO molecule in chemdraw. Using gaussian98 I
calculated the atomic charges. I have successfully created the DMSO unit.
Following the construction of the peptide unit I went ahead solvating the
solute into the solvent using the following commands:
set <solvent unit> restype solvent
set <solvent unit> vdw
solvatebox <peptide unti> <solvent unit> 10.0

Upon checking the created box I had some warnings of close contacts between
some atoms of the DMSO and the peptide but the final message was Unit OK.

When I tried to run the minimasation in amber7 it started running but in the
output file it failed to write anything beyond the lines:

Max Nonbonded Pairs:72000000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

The error message writes:
forrtl: error (75): floating point exception
   0: __FINI_00_remove_gp_range [0x3ff81a6c1a4]
   1: __FINI_00_remove_gp_range [0x3ff81a7405c]
   2: __FINI_00_remove_gp_range [0x3ff800d0b8c]
   3: dihpar_

I have successfully executed a minimasation using the same peptide in a
water box. I compared the .lib .prm and .pdb files with those of the
peptide+DMSO box and cannot find any difference. The only difference is
that I created the DMSO box in the presence of the peptide unit.

Do I have to create the DMSObox before solvating? Does anyone know how to
create a DMSObox from the DMSO unit without the presence of a solute unit?

Thanks in advance.

Best wishes,

John

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