[gmx-users] updating amberff.03 files

[Mark Abraham]

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 <lkingsle at 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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