Hi Mark,

We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work in the new version? 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.



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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--
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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