[gmx-users] pdb2gmx problem

[Warren Gallin]

Hi,

	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.

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

	pdb2gmx -f Gly10_Capped.pdb -water tip3p -ignh

	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
WARNING: masses will be determined based on residue and atom names,
          this can deviate from the real mass of the atom type
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/atommass.dat
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
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading Gly10_Capped.pdb...
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
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
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/ffoplsaa.rtp
Residue 56
Sorting it all out...
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
Processing chain 1 (44 atoms, 12 residues)
There are 11 donors and 11 acceptors
There are 21 hydrogen bonds
Checking for duplicate atoms....
Opening library file /opt/local/var/macports/software/gromacs/4.0_0/ 
opt/local/share/gromacs/top/specbond.dat
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
-------------------------------------------------------

	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.

	Can someone shed some light on this?


Warren Gallin

-------------- next part --------------
A non-text attachment was scrubbed...
Name: Gly10_Capped.pdb
Type: application/octet-stream
Size: 3168 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090828/6f776b0f/attachment.obj>
-------------- next part --------------