On 4/26/12 7:45 AM, Delmotte, Antoine wrote:
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:
O
|
(...)--CH2--O--P--O--H
|
O
(details of the whole molecule here:
http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAP&sid=1RBO
<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?
The problem isn't necessarily the atom types themselves (which seem to be
reasonable enough from the information provided), but rather that there are no
default bonded parameters for these interactions. If you look into
ffnonbonded.itp, the second column is entitled "bond_type" and thus refers to
the names used by grompp when interpreting how atoms are connected. The actual
bond, angle, and dihedral parameters are in ffbonded.itp, using these names.
You would have to map out what the bond_type names are for each of these and
find/derive new parameters for each of the interactions that are missing.
-Justin
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 ]
HO2P O2P
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
O5P HO5P
Thank you very much in advance!
Antoine
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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