AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Sep 14 2009 - 10:04:58 CDT

Abhishek,

>     Thanks for your file.  Actually I was trying to use OPLSAA force
> field. I was wrong. Now with DMF and MEOH mol2 file I have created
> DMF.off and MEOH.off file with modified script1.ff.

You do not need to create off files. mol2 files can be directly used.

> I created the solvant box with DMF. Then I edited what you told me to do.

You need to modify the DMF molecules (in the 100 % DMF box) with an
_even_ residue number i.e. DMF molecule numbers 2, 4, 6, 8 etc...
Do not modify all of them. See below.

regards, Francois

ATOM 1 N1 DMF 1 0.3368 -0.0218 -0.0000
ATOM 2 C1 DMF 1 0.4248 1.4218 0.0000
ATOM 3 H11 DMF 1 0.9563 1.7698 0.8808
ATOM 4 H12 DMF 1 0.9563 1.7699 -0.8808
ATOM 5 H13 DMF 1 -0.5709 1.8333 0.0000
ATOM 6 C2 DMF 1 1.5744 -0.7627 0.0000
ATOM 7 H21 DMF 1 1.3729 -1.8258 -0.0000
ATOM 8 H22 DMF 1 2.1660 -0.5279 -0.8799
ATOM 9 H23 DMF 1 2.1660 -0.5279 0.8799
ATOM 10 C3 DMF 1 -0.8637 -0.6366 0.0000
ATOM 11 H3 DMF 1 -0.7770 -1.7237 0.0000
ATOM 12 O4 DMF 1 -1.9300 -0.0938 0.0000
TER
ATOM XX O2 MEO 2 Other of Cartesian coordinates
TER
ATOM YY N1 DMF 3 Other of Cartesian coordinates
ATOM YY C1 DMF 3
ATOM YY H11 DMF 3
ATOM YY H12 DMF 3
ATOM YY H13 DMF 3
ATOM YY C2 DMF 3
ATOM YY H21 DMF 3
ATOM YY H22 DMF 3
ATOM YY H23 DMF 3
ATOM YY C3 DMF 3
ATOM YY H3 DMF 3
ATOM YY O4 DMF 3
TER
ATOM ZZ O2 MEO 4 Other of Cartesian coordinates
TER

etc...
END

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