[gmx-users] topology file for small organic molecule

[Yunfeng Hu]

Hi, I am trying to build a topology file for an antibody substrate 
using pdb2gmx -f test.pdb -p test.top -o test.gro. I got the following 
error. Why does the program complain about the residue name since I am 
using OPLS for small molecule only. Thanks.

Eric

Reading test.pdb...
Read 43 atoms
Opening library file /Users/yunfenghu/gromacs3.2/share/top/xlateat.dat
19 out of 19 lines of xlateat.dat converted succesfully
Opening library file 
/Users/yunfenghu/gromacs3.2/share/top/aminoacids.dat
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 43 atoms

   chain  #res #atoms
   1 'C'     1     43

All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /Users/yunfenghu/gromacs3.2/share/top/FF.dat

Select the Force Field:
  0: Gromacs Forcefield (see manual)
  1: Gromacs Forcefield with all hydrogens (proteins only)
  2: GROMOS96 43a1 Forcefield (official distribution)
  3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
  4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
5
Using ffoplsaa force field
Opening library file /Users/yunfenghu/gromacs3.2/share/top/ffoplsaa.atp
Atomtype 696
Reading residue database... (ffoplsaa)
Opening library file /Users/yunfenghu/gromacs3.2/share/top/ffoplsaa.rtp
Residue 50
Sorting it all out...
Opening library file /Users/yunfenghu/gromacs3.2/share/top/ffoplsaa.hdb
Opening library file 
/Users/yunfenghu/gromacs3.2/share/top/ffoplsaa-n.tdb
Opening library file 
/Users/yunfenghu/gromacs3.2/share/top/ffoplsaa-c.tdb
Processing chain 1 'C' (43 atoms, 1 residues)
Opening library file /Users/yunfenghu/gromacs3.2/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Fatal error: Residue 'XXX' not found in residue topology database

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Yunfeng Hu, Ph.D
Research Associate
Department of Molecular Biology, MB-5
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037
Tel. (858) 784-2204
Fax. (858) 784-2860
Emal: yunfeng at scripps.edu
Web: http://www.scripps.edu/~yunfeng
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