[gmx-users] updating amberff.03 files

Laura Kingsley lkingsle at purdue.edu
Thu Apr 11 22:36:25 CEST 2013

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.


- 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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