[gmx-users] Carbohydrate MD Simulation

Nancy nancy5villa at gmail.com
Fri Jul 31 22:44:38 CEST 2009


I am trying to run a MD simulation on trehalose (glucose disaccharide) in
water.  I obtained the PDB file from the URL:
http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb .  When I run pdb2gmx on
the PDB file:

pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v

I chose force field 5 (OPLS) from the list:

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

And I received the following error message:

Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms
             while sorting atoms

Please help.

Thank you,

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