So if I'm understanding you correctly in the .rtp file under
[ HEME ]
[ dihedrals ]
I should change:
HP42 CBD CGD O1D
HP42 CBD CGD O2D
...
to
HP42 CBD CGD O1D 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000
HP42 CBD CGD O2D 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000
Do I need to remove these definitions from the ffbonded.itp files then?
- Laura
On 04/11/2013 05:43 PM, Mark Abraham wrote:
On Thu, Apr 11, 2013 at 11:14 PM, Laura Kingsley<lking...@purdue.edu>wrote:
Hi Mark,
We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work in
the new version?
Sorry, I was thinking of 4 and 9, which are basically interchangeable. The
default for AMBER did change to 9 at some point (see top of
aminoacids.rtp). You can use the old approach if you change the types of
just the heme dihedrals to 3 in the .itp files produced by pdb2gmx. Or you
can probably edit the heme .rtp entry to specify type 3 (plus parameters,
perhaps via the #defines).
Also, I took out the #define lines and replaced them with the actual
atomtypes, because that didn't seem to work when I initially tried to add
just the #define lines to the ffbonded.itp file.
The parameters need to go either on the lines in the .rtp that define the
interactions, or on the lines that define the dihedraltypes. Only the
latter needs the atom types (because that's how the lookup works). The
old-style #defines cannot work in ffbonded.itp, because they assume the
context of the .rtp, where the atoms are already identified.
Mark
On 04/11/2013 04:51 PM, Mark Abraham wrote:
Type 9 was added at some point to GROMACS to make coping with AMBER and
CHARMM easier. So you should just change your #defines from 3 to 9. See
table in chapter 5. Or you could just leave your solution in the same form
as you did for the 4.0.x GROMACS.
Mark
On Thu, Apr 11, 2013 at 10:36 PM, Laura Kingsley<lking...@purdue.edu>**
wrote:
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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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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--
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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