[gmx-users] OPLSAA + NAC-ACE

[Pawan Babel]

Hi all
I am using OPLSAA forcefield with explicit water model on gromacs 3.2.1
with NAC & ACE terminal as capping my peptide chain.

During pdb2gmx i am getting following error :
Fatal error: Atom CH3 in residue NAC 15 not found in rtp entry with 6 atoms
             while sorting atom

============details of my commands and procedure
[pawan at lysozyme helix]$ pdb2gmx -f pep.pdb -p pep.top -o pep.gro -inter -ignh
                         :-)  G  R  O  M  A  C  S  (-:

           Glycine aRginine prOline Methionine Alanine Cystine Serine

                            :-)  VERSION 3.2.1  (-:

Select the Force Field:
 0: GROMOS96 43a1 Forcefield (official distribution)
 1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
 2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3:
OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 4: Gromacs Forcefield (see manual)
 5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
3
Looking whether force field file ffoplsaa.rtp exists
Opening library file /usr/local/share/gromacs/top/ffoplsaa.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading pep.pdb...
Read 119 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 15 residues with 119 atoms

  chain  #res #atoms
  1 'A'    15    119

All occupancies are one
Opening library file /usr/local/share/gromacs/top/ffoplsaa.atp
Atomtype 700
Reading residue database... (ffoplsaa)
Opening library file /usr/local/share/gromacs/top/ffoplsaa.rtp
Residue 53
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffoplsaa.hdb
Opening library file /usr/local/share/gromacs/top/ffoplsaa-n.tdb
Opening library file /usr/local/share/gromacs/top/ffoplsaa-c.tdb

Back Off! I just backed up pep.top to ./#pep.top.8#
Processing chain 1 'A' (119 atoms, 15 residues)
Which LYSINE type do you want for residue 8
0. Not protonated (charge 0) (LYS)
1. Protonated (charge +1) (LYSH)

Type a number:1
Which ASPARTIC ACID type do you want for residue 7
0. Not protonated (charge -1) (ASP)
1. Protonated (charge 0) (ASPH)

Type a number:0
Which GLUTAMIC ACID type do you want for residue 2
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)

Type a number:0
Which GLUTAMIC ACID type do you want for residue 5
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUH)

Type a number:0
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Fatal error: Atom CH3 in residue NAC 15 not found in rtp entry with 6 atoms
             while sorting atoms
================================================================== Now i
check my defualt entry of ffoplsaa files in .../gromacs/top
directory.

Default entry in ffoplsaa.hdb for ACE and NAC in gromacs 3.2.1 are : NAC  
  2
        1       1       N       -C      CH3
        3       4       CH3     N       -C

ACE     1
        3       4       CH3     C       O
=========================================
and default entry in ffoplsaa.itp for ACE and NAC are:
[ ACE ]
 [ atoms ]
    CA    opls_135   -0.180     1
  HH31    opls_140    0.060     1
  HH32    opls_140    0.060     1
  HH33    opls_140    0.060     1
     C    opls_235    0.500     2
     O    opls_236   -0.500     2
 [ bonds ]
    CA  HH31
    CA  HH32
    CA  HH33
    CA     C
     C     O
[ impropers ]
  CA    +N    C      O     improper_O_C_X_Y

[ NAC ] ; metylamide, a.k.a NMA.
 [ atoms ]
     N    opls_238   -0.500     1
     H    opls_241    0.300     1
    CA    opls_242    0.020     2
  HH31    opls_140    0.060     2
  HH32    opls_140    0.060     2
  HH33    opls_140    0.060     2
 [ bonds ]
     N     H
     N    CA
    CA  HH31
    CA  HH32
    CA  HH33
    -C     N
 [ impropers ]
    -C    CA    N    H      improper_Z_N_X_Y
===========================================================
But can anyone explain me why there are different nomenclature in
ffoplsaa.hdb and ffoplsaa.itp ?

seeing different nomenclature used in ffoplsaa.hdb and ffoplsaa.itp for
alpha carbon. So i modified the my ffoplsaa.rtp file by replacing CA by
CH3.
Now it does not any error during pdb2gmx but it shows error during grompp.
WARNING 1 [file "pep.top", line 1551]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 2 [file "pep.top", line 2161]:
  No default Ryckaert-Bell. types, using zeroe

My modified ffoplsaa.rtp with ACE and NAC as :
===================ffoplsaa.rtp ------------
[ ACE ]
 [ atoms ]
   CH3    opls_135   -0.180     1
  HH31    opls_140    0.060     1
  HH32    opls_140    0.060     1
  HH33    opls_140    0.060     1
     C    opls_235    0.500     2
     O    opls_236   -0.500     2
 [ bonds ]
   CH3  HH31
   CH3  HH32
   CH3  HH33
   CH3     C
     C     O
[ impropers ]
  CH3    +N    C      O     improper_O_C_X_Y


[ NAC ] ; metylamide, a.k.a NMA.
 [ atoms ]
     N    opls_238   -0.500     1
     H    opls_241    0.300     1
   CH3    opls_242    0.020     2
  HH31    opls_140    0.060     2
  HH32    opls_140    0.060     2
  HH33    opls_140    0.060     2
 [ bonds ]
     N     H
     N   CH3
   CH3  HH31
   CH3  HH32
   CH3  HH33
    -C     N
 [ impropers ]
    -C    CH3     N    H      improper_Z_N_X_Y
======================================================

Any help is greatly appreciated.
Thanks
Pawan Babel