hi Francois
Actually now I have some other problem. First I loaded the mol2 with
/opt/amber/amber9/exe/xleap -s -f script1.ff , so DMF and MEOH both loaded. Now I created a box with solvateoct MEOH DMF buffer, buffer I adjusted so i will be in 1:1 ratio. I save that as xx.pdb. But When I am trying to load that xx.pdb its truncating MEOH -> MEO and I am getting some dots for MEOH. DMF is fine. I want ot use this pdb to create the mixture box . how to handle this problem.
thanx
abhishek
--- On Mon, 14/9/09, FyD <fyd.q4md-forcefieldtools.org> wrote:
From: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: [AMBER] DMF solvent box
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Monday, 14 September, 2009, 3:04 PM
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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Received on Tue Sep 15 2009 - 22:00:02 PDT
