[gmx-users] pdb2gmx problem

[Warren Gallin]

Hi,




        I built the PDB file using TINKER (see attached file) but when I run:

        pdb2gmx -f Gly10_Capped.pdb -water tip3p -ignh




WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type

Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type

Entries in vdwradii.dat: 28

Entries in dgsolv.dat: 7

Entries in electroneg.dat: 71

Entries in elements.dat: 218
Reading Gly10_Capped.pdb...

26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 12 residues with 44 atoms

  chain  #res #atoms
  1 ' '    12     44

All occupancy fields zero. This is probably not an X-Ray structure

Atomtype 1
Reading residue database... (ffoplsaa)

Residue 56
Sorting it all out...

Processing chain 1 (44 atoms, 12 residues)
There are 11 donors and 11 acceptors
There are 21 hydrogen bonds
Checking for duplicate atoms....

7 out of 7 lines of specbond.dat converted succesfully
N-terminus: NH3+
C-terminus: COO-
Now there are 12 residues with 79 atoms

-------------------------------------------------------
Program pdb2gmx, VERSION 4.0
Source code file: pdb2top.c, line: 574

Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
-------------------------------------------------------



        Can someone shed some light on this?


Warren Gallin

I am trying to set up a simulations of short peptides in water, and I want to eliminate the electrostatic interactions of the N-terminal amino group and the C-terminal carboxyl group by capping them, with acetate for the N-terminus and a C-terminal amide. and I selected the OPLSAA/L force field (option 5) when prompted, and process continues, terminating in a fatal error: Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/ffoplsaa.rtp Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/aminoacids.dat Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/aminoacids.dat Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/atommass.dat Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/vdwradii.dat Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/dgsolv.dat Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/electroneg.dat Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/elements.dat Read 'Protein Gly10_Capped built with TINKER/Force Field Explorer', 44 atoms Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/xlateat.dat Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/ffoplsaa.atp Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/ffoplsaa.rtp Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/ffoplsaa.hdb Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/ffoplsaa-n.tdb Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/ffoplsaa-c.tdb Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ opt/local/share/gromacs/top/specbond.dat The ACE residue does not have a N atom, either in the pdb file or in ffoplsaa.hdb or in ffoplsaa.rtp, so I don't understand what the problem is.

Gly10_Capped.pdb
Description: Binary data

        
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