[gmx-users] opls-aa forcefield niggles

[Graham Smith]

Hi - 

I'm trying to run some opls-aa ff simulations with 3.1.4 and have had
some minor problems: 

(a) by default, I couldn't get it to include ions in the simulations. 
Grompp gives a message like 
Fatal error: No such moleculetype CL

I found I could fix this by adding 
#ifdef _FF_OPLS
[ moleculetype ]
; molname	nrexcl
CL            1 
[ atoms ]
; id	at type	res nr 	residue name	at name  cg nr	charge   mass
1	opls_401	1	CL	 CL	 1   -1.000  35.45300
 
etc etc for the rest of them

#endif 

in the ions.itp 

(b) if I have a C-terminal GLY, I can't get COO- without ending up 
with non-integral charge. pdb2gmx -ter doesn't seem to offer me the
special [ GLY-COO- ] option that is in the tdb. COOH is OK. 

Cheers, 

-Graham 

########################################################################

Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5737            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr