AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Sep 16 2009 - 00:09:42 CDT

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_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
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> Love Cricket? Check out live scores, photos, video highlights
> and more. Click here http://cricket.yahoo.com
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber