AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: Abhishek Banerjee (a.banerjee_at_ymail.com)
Date: Thu Sep 17 2009 - 01:15:53 CDT

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

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