[gmx-users] Problem with Atom type

[David van der Spoel]

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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