Hello Gromacs Users,
I am trying to update the contents of the top folder. I have parameters
for a HEME residue that worked in gromacs 4.0.7, and we're now trying to
update to gromacs 4.6.1 (long overdue), and need to migrate the
parameters over to the new version.
I have done the following:
1. added the HEME atomtypes to the atomtypes.atp file
2. added the hydrogens to the aminoacids.hdb file
3. added the [ HEME ] block to the aminoacids.rtp file
I am running into problems in adding the dihedrals. in the old version
we had used #define statements in the ffamber03bon.itp file
(ffbonded.itp in the 4.6 version) , for example:
#define heme_1 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000
#define heme_2 0.62760 1.88280 0.00000 -2.51040
0.00000 0.00000
#define heme_3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000
#define heme_4 16.52680 0.00000 -16.52680 0.00000
0.00000 0.00000
#define heme_5 62.76000 0.00000 -62.76000 0.00000
0.00000 0.00000
the "heme_X" term was defined in the ffamber03.rtp file (aminoacids.rtp
file in ver 4.6)- for example:
[ dihedrals ]
HP42 CBD CGD O1D heme_1
HP42 CBD CGD O2D heme_1
HP41 CBD CGD O1D heme_1
HP41 CBD CGD O2D heme_1
HP52 CAD CBD HP41 heme_2
HP52 CAD CBD HP42 heme_2
HP52 CAD CBD CGD heme_3
I updated all "define heme_X" lines in the ffbonded.itp file by going
back and putting in the actual atomtypes and the corresponding dihedral
function and parameters. For example:
I replaced
#define heme_8 11.92440 0.00000 -11.92440 0.00000
0.00000 0.00000
with :
FE NO CC CD 3 11.92440 0.00000 -11.92440
0.00000 0.00000 0.00000
However, I'm getting errors from the grompp command about the
dihedrals. it gives:
ERROR 1 [file prot_Other_chain_B2.itp, line 520]:
No default Proper Dih. types
ERROR 2 [file prot_Other_chain_B2.itp, line 521]:
No default Proper Dih. types
.
.
.
I'm thinking that it can't find the Dihedral types that I added t the
ffbonded.itp file, but I'm not sure why. One thing I've noticed is that
in the .itp file generated by pdb2gmx the dihedral type for the heme is
given as a 9, but in the ffbonded.itp file, I specify it as a 3. I'm not
sure where its reading this from.
I'm hoping that this is just a simple thing that I'm missing and someone
can help point me in the right direction.
Thanks,
- Laura
--
Laura Kingsley
Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643
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