[gmx-users] Free energy and pdb2gmx

carmien at alumni.uv.es carmien at alumni.uv.es
Thu Sep 2 18:12:49 CEST 2004

 Dear all,

I'm working with gromacs to calculate the solvation free energy of
Benzen, Toluene, D and L-arginine and many others in water. I use
different box sizes to each one.

I have two questions:


Since I can calculate the solvatione free energy using thermodinamic
integration or perturbation, does anybody know which method provides
more accurately results?? (I don't have experimental data for the
different size boxes...)


This second question is only related with D and L-arginine. I downloaded
several .pdb files in order to create the top and .gro files. My problem
appears when I execute the following command line:

                              pdb2gmx  -f  D(or L)-arginine.pdb

There's a Fatal Error message at the end of the process, as you can see

Opening library file /usr/local/gromacs/share/top/FF.dat
 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)
 6: Corse-Graine Force Field
 Looking whether force field file ffG43a2.rtp exists
 Opening library file /usr/local/gromacs/share/top/ffG43a2.rtp
 Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Reading D-arginine.pdb...
 Read 'February 28, 2002', 27 atoms
 Opening library file /usr/local/gromacs/share/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 1 residues with 27 atoms

 chain s #res #atom
   1 ' '     1     27=20

 All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/local/gromacs/share/top/ffG43a2.atp
Atomtype 50
 Reading residue database... (ffG43a2)
 Opening library file /usr/local/gromacs/share/top/ffG43a2.rtp
 Residue 96
 Sorting it all out...
 Opening library file /usr/local/gromacs/share/top/ffG43a2.hdb
Opening library file /usr/local/gromacs/share/top/ffG43a2-n.tdb
 Opening library file /usr/local/gromacs/share/top/ffG43a2-c.tdb
 Processing chain 1 (27 atoms, 1 residues)
 Opening library file /usr/local/gromacs/share/top/specbond.dat
 5 out of 5 lines of specbond.dat converted succesfully
 There are 4 donors and 2 acceptors
 There are 1 hydrogen bonds
 Fatal error: Residue '' not found in residue topology database

The fact is I don't know who is that '', because I cannot find any tails
 inside my .pdb files, and the message appears for all the .pdb files.
 What do I have to do? Any suggestion will be gratefull,


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