AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: Abhishek Banerjee (a.banerjee_at_ymail.com)
Date: Tue Sep 15 2009 - 23:33:23 CDT

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_at_q4md-forcefieldtools.org> wrote:

From: FyD <fyd_at_q4md-forcefieldtools.org>
Subject: Re: [AMBER] DMF solvent box
To: "AMBER Mailing List" <amber_at_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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