[gmx-users] Atom types for phosphate group in OPLS-AA force field

Delmotte, Antoine antoine.delmotte09 at imperial.ac.uk
Thu Apr 26 13:45:56 CEST 2012

Dear Gromacs users,

I am here requesting your help with regards to the editing of the 
OPLS-AA force field, and more specifically, the choice of the atom types.

I have added an entry for the molecule CABP to the .rtp and .hdb files.

I can run pdb2gmx, genbox and editconf without getting any error. 
However, when I run grompp, I receive the following errors:

ERROR 1 [file 1RBO_Protein_chain_A.itp, line 15054]:
No default Bond types

ERROR 78 [file 1RBO_Protein_chain_M.itp, line 47276]:
No default Angle types

ERROR 82 [file 1RBO_Protein_chain_M.itp, line 66639]:
No default Ryckaert-Bell. types

(there are 160 of those).

 From what I could see in this mailing list, it seems the error comes 
from the choice of the atom types for the phosphate groups. I have tried 
several of them which seemed to make sense, but none of them allowed to 
remove all the errors.

The end of the chain is something like:


(details of the whole molecule here: 
<http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAP&sid=1RBO> )

The problem is about the atom type of the -OH group at the end. Here are 
the entries from the .atp file which I thought were relevant:

opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2
opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2
opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate
opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG
opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2

I chose opls_445 for the P, opls_446 for the 3 oxygens, and opls_449 for 
the hydrogen. Apparently, I got it wrong for the oxygen and the hydrogen 
of the OH group, at least. Unless the error actually comes from 
something else...

So my question is the following: Have I done something wrong about the 
atom types? If so, does anyone know which atom type I should choose?

Details of my rtp entry:

[ CAP ]
[ atoms ]
P1 opls_445 1.539429 1
O1P opls_446 −0.818751 1
O2P opls_446 −0.899293 1
HO2P opls_449 0.429028 1
O3P opls_446 −0.895147 1
O1 opls_447 −0.772438 2
C1 opls_448 0.022084 3
HC11 opls_449 0.176920 3
HC12 opls_449 0.139342 3
C2 opls_159 0.146383 4
O2 opls_154 −0.883774 4
HO2 opls_155 0.527657 4
C opls_271 0.815849 5
O6 opls_271 −0.766517 5
O7 opls_272 −0.771422 5
C3 opls_158 0.142583 6
HC3 opls_140 0.107158 6
O3 opls_154 −0.817159 6
HO3 opls_155 0.471262 6
C4 opls_158 0.184473 7
HC4 opls_140 0.164192 7
O4 opls_154 −0.822792 7
HO4 opls_155 0.498509 7
C5 opls_448 0.038563 8
HC51 opls_449 0.143027 8
HC52 opls_449 0.135804 8
O5 opls_447 −0.730025 9
P2 opls_445 1.526672 10
O4P opls_446 −0.866625 10
O5P opls_446 −0.810148 10
HO5P opls_449 0.521464 10
O6P opls_446 −0.876311 10
[ bonds ]
O1P P1
O2P P2
O3P P1
P1 O1
O1 C1
C1 HC11
C1 HC12
C1 C2
C2 O2
O2 HO2
C2 C
C O6
C O7
C2 C3
C3 O3
C3 HC3
O3 HO3
C3 C4
C4 HC4
C4 O4
O4 HO4
C4 C5
C5 HC51
C5 HC52
C5 O5
O5 P2
P2 O4P
P2 O5P
P2 O6P

Thank you very much in advance!


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