[gmx-users] Still Problem with Atom type Molybdenum

[Dastmalchi]

Dear All,

As I mentioned already, I have still problem with Molybdenum atom in my
system. Just for the sake of test I have a 4-atom molecule like MoO2S. I
made a gro file of that and then added water molecules. The following is the
TOP file:
###############################
; This is your topology file
; "This Is A Recording" (Your Answering Machine)
; Include forcefield constants
#include "ffgmx.itp"
#include "mos.itp"
[ system ]
; Name
MOS in water
[ molecules ]
; Compound #mols
MOS      1
SOL               126
###############################

I have added the following to ffgmxbon.itp file.
MO    S    1   0.18200     376650.
MO    OA    1   0.20500     376650.

and have fixed atommass.dat and ffgmx.atp files by adding the following
lines in them:
??? MO 95.9400
MO 95.94000 ; molybdenum

I have done all of these for Gromacs running under UNIX (IRIX) and Windows
operating systems. However I am getting the same error in both systems
saying:
Fatal error: Atomtype 'MO' not found!

I will appreciate it if you help me out with this.

CHeers, Siavoush

> Hi,
>
> Thanks for David, but I am stile getting the same message.
> Any further suggestion?
>
> Thank you all in advance.
>
> Cheers, Siavoush
>
> ----- Original Message -----
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Thursday, December 18, 2003 7:31 PM
> Subject: Re: [gmx-users] Problem with Atom type
>
>
> > On Thu, 18 Dec 2003, Dastmalchi wrote:
> >
> > >Hi GMX users,
> > >
> > >I am dealing with a system which has a Molybdenum-containing cofactor
in
> it. I have written a "itp" file for this cofactor, and included that in my
> top file and tried to use it, but I am getting error, saying that it can't
> find the atom type 'MO' for the grompp command.
> > >Here is the few last line of the message:
> > >
> > >Processing topology .
> > >
> > >Generated 1125 of the 1326 nonbonded parameter combination
> > >
> > >Cleaning up temporarily file grompp001302
> > >
> > >Fatal error: atom type 'MO' not found!
> > >
> > >
> >
> > ffgmxnb.itp
> >
> >
> > >
> > >I have named the molybdenum atom MO and have added the following line
> into atommass.dat files:
> > >??? MO 95.9400
> > >I have also added a line into ffgmx.atp file:
> > >MO 95.94000 ; molybdenum
> > >At the end of email I have put the content of the itp file for the
> cofactor called MOS.
> > >
> > >1) Would you please let me know if the itp file is OK? I didn't add any
> values for bonds, angles and dihedrals. Are those info necessary?
> > >
> > >2) Is there any further changes that I need to do? i.e. to add a
> necessary info into a particular file.
> > >
> > >
> > >Many thanks for your help.
> > >
> > >Cheers, Saivoush
> > >
> > >
> > >
> > >[ moleculetype ]
> > >;name nrexcl
> > >MOS 3
> > >[ atoms ]
> > >; nr type resnr resid atom cgnr charge
> > >1 MO 1 MOS MO  1 0.474
> > >2  S 1 MOS S   1 -0.125
> > >3 OA 1 MOS O1  1 -0.397
> > >4 OA 1 MOS O2  1 -0.372
> > >5 HS 1 MOS HAA 1 0.199
> > >6 HS 1 MOS HAB 1 0.221
> > >[ bonds ]
> > >;ai aj fu
> > >1 2 1
> > >1 3 1
> > >1 4 1
> > >3 5 1
> > >4 6 1
> > >[ angles ]
> > >;ai aj ak fu
> > >2 1 3 1
> > >2 1 4 1
> > >1 3 5 1
> > >1 4 6 1
> > >3 1 4 1
> > >[ dihedrals ]
> > >;ai aj ak al fu
> > >2 1 3 5 1
> > >2 1 4 6 1
> > >5 3 1 4 1
> > >6 4 1 3 1
> >
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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