[gmx-developers] Re: Amber to Gromacs forcefield conversion

[Graham Smith]

Anton Feenstra wrote :

> I've just now commited my amber2gmx forcefield comversion scripts to the
> CVS in src/contrib/scripts. 

> Known bugs and problems at this moment are:  - pairs, grompp says: no
> defaults. That is reasonable, since no
> pairtypes are defined yet. I have to look up how they are defined
>  in the Amber ff. I think it is simply a scaling with respect to
>  the normal LJ parameters.
>- impropers: a trial EM run on a peptide results in distorted
>  geomoetry. Nothing definite yet, but it seems the impropers are off.

I did
pdb2gmx -f 4pti.pdb -o 4pti1.pdb -p 4pti1.top -i 4pti1.itp -ss -ter 
grompp -f mdmin.mdp -c 4pti1.pdb -p 4pti1.top -o 4pti1.tpr \
-maxwarn 10000
which works after a fashion, then I gmxdumped the tpr.

CYS S-S briges don't work yet. 
I had to rename LYS, LYN -> LYSH, LYS in .hdb 

As you say, the impropers aren't right yet - the angle and force constant
are the wrong way round. More worryingly, these are just the impropers for
pi-bonding: the impropers that maintain the geometry of chiral centres are
missing, and I can't see them in the amber force field files either - are
they generated automatically by amber? Maybe we should just generate one
for every sp3-hybridized atom (...that doesn't have two or three hydrogens
on it)? 

My -n and -c.tdb files nearly work, once I renamed peptide hydrogen from
HN to H. There was a weird error with an N-terminal R, which I suspect
may be a bug; almost every atom has to be in the [replace] list, and pdb2gmx 
complained about just the 2nd H atom on every heavy atom:
WARNING: atom HB2 is missing in residue ARG 1 in the pdb file
         You might need to add atom HB2 to the hydrogen database of
         residue ARG
         in the file ff???.hdb (see the manual)
WARNING: atom HG2 is missing in residue ARG 1 in the pdb file
WARNING: atom HD2 is missing in residue ARG 1 in the pdb file
WARNING: atom HH12 is missing in residue ARG 1 in the pdb file
WARNING: atom HH22 is missing in residue ARG 1 in the pdb file
It tolerates the HA on CA though. 
(they *are* there in hdb and have right name) 

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 5734            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr