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

--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to