[gmx-users] Problem with Atom type

[Dastmalchi]

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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