hi Francois
Hi I have created the box at last. But I can't save the parameter as prmtop and inpcrd. For DMF its showing bond C-H1 not found ( the problem is H1 in C=O). I checked ff99..dat and I assigned atom type for DMF according to that in script.ff . plz help ME.\
Thanks
abhishek
--- On Wed, 16/9/09, 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: Wednesday, 16 September, 2009, 5:09 AM
Abhishek,
> 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.
replace the residue name MEOH by MEO in
http://q4md-forcefieldtools.org/REDDB/projects/W-32/tripos1.mol2
You can also add the Cornell et al. FF atom types: It takes 3 sec.
see below
regards, Francois
.<TRIPOS>MOLECULE
MEO
6 5 1 0 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 H11 -1.076631 0.975959 0.000000 H1 1 MEO 0.0234
2 C1 -0.655546 -0.019723 0.000000 CT 1 MEO 0.1686
3 H12 -1.012856 -0.543375 -0.883547 H1 1 MEO 0.0234
4 H13 -1.012855 -0.543375 0.883547 H1 1 MEO 0.0234
5 O2 0.736965 0.120595 0.000000 OH 1 MEO -0.6652
6 H2 1.139896 -0.735629 0.000000 HO 1 MEO 0.4262
.<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 2 4 1
4 2 5 1
5 5 6 1
.<TRIPOS>SUBSTRUCTURE
1 MEO 1 **** 0 **** ****
> --- 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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>
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>
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Wed Sep 16 2009 - 23:30:02 PDT
