AMBER Archive (2003)

Subject: Re: AMBER: DMSO box

From: Jiten (jiten_at_postech.ac.kr)
Date: Fri Sep 12 2003 - 20:05:46 CDT

Hello,

You can try the following commnds in xleap

>DMSOBOX = copy DMSO (DMSO is your DOMO unit)
>set DMSO restype DMSO solvent
>solvatebox DMSOBOX DMSO n ( n could be 5, 10 or any value, it gives the
box size)

I hope it would be better idea to equilibrate DMSO before solvating the
peptide unit. Check if you get the proper density when you are equilibrating
DMSO alone.

I hope this helps.

Best wishes,

N. Jiten Singh
C/O Prof. Kwang S. KIm
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e

----- Original Message -----
From: "Dalmaris, John" <john.dalmaris_at_imperial.ac.uk>
To: <amber_at_scripps.edu>
Sent: Friday, September 12, 2003 6:25 PM
Subject: AMBER: DMSO box

> 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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