[gmx-users] Re: gmx-users digest, Vol 1 #938 - 12 msgs

[David van der Spoel]

On Tue, 2003-08-19 at 20:29, Mr.Sridhar wrote:
> Dear GMX users,
> 
> Iam doing MD on a protein containing heme cofactor.  But some
> of the bond types, bond angles and dihedral angles in the heme are not
> getting recognised. The folowing warnings were displayed.
> 
> #########################################
> No default G96Bond types, using zeroes.
> No default G96Angle types, using zeroes.
> No default Proper Dih. types, using zeroes.
> ###########################################
> 
> The bond type that is not recognised was between SG of CYS in protein  and
> FE of HEME.
> The angle types that were not recognised were between SG-FE-NR; SG of CYS
> FE and NR of HEME.
> The dihedral type that were not recognised was between CH1-CH2-SG-FE ;
> CH1, CH2 of CYS and FE of HEME
> 
> The dynamics ran succesfully, but I doubt this usage of zeroes for these
> types would affect correct running of Simulation.
> 
> I'll be very grateful to you if you suggest me how to overcome this
> problem.
There are parameters for these interactions in the ffgmx force field
(ffgmxbon.itp). Please add these to your top file.

You definitely don't want bond lengths of zero, so check the distance
between sulphur and iron after simulation.
> 
> 
> Thank you.
> 
> sridhar
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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