[gmx-users] Interactive GLU selection and dihedrals
Ivano.Eberini at unimi.it
Tue May 21 16:42:41 CEST 2002
> 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).
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
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:
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
Thanks for your suggestions and kindness.
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