[gmx-users] Re: gmx-users Digest, Vol 45, Issue 29

Mon Jan 14 18:00:12 CET 2008

Dear users,
            I tried the prodrg beta version as well, but i still dont understand, it does consider 
the aromatic hydrogens but deletes the polar hydrogens on the H2PO3- groups.
I am adding the pdb file under please do help if you can. 

ATOM      1  C1  FNP X 301      43.226  14.934  14.797  1.00 44.35           C
ATOM      2  C2  FNP X 301      44.293  10.378  18.585  1.00 46.18           C
ATOM      3  C3  FNP X 301      43.672   9.449  17.765  1.00 45.78           C
ATOM      4  C4  FNP X 301      43.020   9.807  16.600  1.00 46.76           C
ATOM      5  C5  FNP X 301      42.973  11.154  16.208  1.00 44.76           C
ATOM      6  C6  FNP X 301      42.316  11.539  15.028  1.00 45.10           C
ATOM      7  C7  FNP X 301      42.279  12.860  14.658  1.00 40.66           C
ATOM      8  C8  FNP X 301      42.872  13.827  15.410  1.00 43.25           C
ATOM      9  C9  FNP X 301      43.543  13.479  16.610  1.00 42.55           C
ATOM     10  C10 FNP X 301      43.595  12.136  17.015  1.00 42.79           C
ATOM     11  C11 FNP X 301      44.247  11.734  18.197  1.00 44.68           C
ATOM     12  C12 FNP X 301      44.591  10.019  19.824  1.00 47.63           C
ATOM     13  F1  FNP X 301      43.227  16.081  15.714  1.00 50.37           F
ATOM     14  F2  FNP X 301      44.408  14.813  14.265  1.00 49.42           F
ATOM     15  P1  FNP X 301      42.067  15.861  13.661  1.00 44.69           P
ATOM     16  OP1 FNP X 301      40.877  15.050  13.339  1.00 39.80           O
ATOM     17  OP2 FNP X 301      42.755  16.211  12.386  1.00 36.98           O
ATOM     18  OP3 FNP X 301      41.592  17.133  14.280  1.00 41.94           O
ATOM     19  F3  FNP X 301      43.581   9.096  20.394  1.00 48.34           F
ATOM     20  F4  FNP X 301      44.725  11.047  20.617  1.00 48.68           F
ATOM     21  P2  FNP X 301      45.850   8.709  20.178  1.00 48.40           P
ATOM     22  OP4 FNP X 301      45.680   7.563  19.249  1.00 46.60           O
ATOM     23  OP5 FNP X 301      45.707   8.197  21.564  1.00 48.03           O
ATOM     24  OP6 FNP X 301      47.227   9.248  20.030  1.00 44.37           O
ATOM     25  H3  FNP X 301      43.699   8.397  18.049  1.00  0.00           H
ATOM     26  H4  FNP X 301      42.542   9.044  15.986  1.00  0.00           H
ATOM     27  H6  FNP X 301      41.834  10.786  14.404  1.00  0.00           H
ATOM     28  H7  FNP X 301      41.763  13.141  13.740  1.00  0.00           H
ATOM     29  H9  FNP X 301      44.017  14.252  17.216  1.00  0.00           H
ATOM     30  H11 FNP X 301      44.726  12.486  18.825  1.00  0.00           H
ATOM     31  HP2 FNP X 301      43.142  17.163  12.454  1.00  0.00           H
ATOM     32  HP3 FNP X 301      42.310  17.862  14.162  1.00  0.00           H
ATOM     33  HP4 FNP X 301      44.891   7.750  18.613  1.00  0.00           H
ATOM     34  HP6 FNP X 301      47.898   8.604  20.473  1.00  0.00           H
END

Message: 2
Date: Thu, 10 Jan 2008 07:18:39 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Generating topology file for a molecule (FNP)
 not in the gromacs library.
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1199967519.47860d1fe290a at webmail.vt.edu>
Content-Type: text/plain; charset=ISO-8859-1

Quoting Mufaddal Soni <muffi_gro at yahoo.com>:

> Dear users,
>                  I am working with PTP1B protein. Recently I tried to
 run it
> in gromacs along with an inhibitor
> {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-
 2-YL]-DIFLUORO-METHYL}-PHOSPHONIC
> ACID    [FNP in short]. The problem is that  gromacs does not
 recognize  FNP
> and hence I am not able to generate a topology file of it using
 pdb2gmx. I
> tried using the The Dundee PRODRG server to generate the topology
 file with
> the pdb file as the input. The problem is that it does generate the
 topology
> file but without any hydrogens. Even the  polar hydrogens information
 is not
> available inspite of it being a part of my input pdb file. Thus I am
 not able
> to use FNP with the polar hydrogens for my runs.
>
> If anyone has faced similar problems please do help if you can.

I know that PRODRG (which I believe uses the old ffgmx) does not add
 aromatic
hydrogens to molecules, but the PRODRG beta site (which uses GROMOS96)
 does. 
You may want to try the beta server, since ffgmx is deprecated (as
 noted in the
manual).

-Justin

>
> Thanking you,
> Cheers.
>
> Soni Mufaddal Saifee,
> B.Tech IIT Madras.
>
>
> ---------------------------------
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  Try it
> now.

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