[gmx-users] Interactive GLU selection and dihedrals

[Ivano Eberini]

> You didn't say which force field, but you need to use:
> 180 69.87 2
> according to the GROMOS96 ff. (see dihedral gd_3 in  ffG43a1bon.itp).

David,
I am using the GROMACS ff, do you think GROMOS96 ff is indeed better for 
MD of proteins in water?
I looked both in ffG43a1bon.itp (GROMOS96) and in ffgmx2bon.itp 
(GROMACS) and I found the following values (they are the same in both 
files):

180.000	16.7		2
; -C-OA- (carboxyl)	4.0

After I defined the CD-OE dihedral, I got another warning about an 
improper dihedral in the same GLUH residue:
'N-C1-C2-C'
I thought it is a tetrahedral to mantain chirality of CA (I hope), so I 
defined it in the [ dihedrals ] section at molecule level:
1401	1403	1405	1415	2	35.264	334.720
;   N		  CA		   CB		   C
Is it correct? (After grompp the warning message disappeared).
Why pdb2gmx does not define this dihedral (all the other ones are 
defined automatically)?

Thanks for your suggestions and kindness.

Ivano