On 24/01/2011 11:53 PM, udaya kiran wrote:
Dear GROMACS users,
I have received the following error when trying to convert a pdb file
(containing N-methylated L- Leucine residue) to gro format. I am
using ffG53a6 forcefield.
Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat
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
4
Opening library file ffG53a6.rtp
Opening library file aminoacids.dat
Opening library file 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 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 vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file electroneg.dat
Entries in electroneg.dat: 71
Opening library file elements.dat
Entries in elements.dat: 218
Reading 16L6_6S17_start.pdb...
WARNING: all CONECT records are ignored
Read '6S17 ', 39 atoms
Opening library file /usr/local/gromacs/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 6 residues with 39 atoms
chain #res #atoms
1 ' ' 6 39
All occupancies are one
Opening library file ffG53a6.atp
Atomtype 1
Reading residue database... (ffG53a6)
Opening library file ffG53a6.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
*-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: resall.c, line: 321
Fatal error:
in .rtp file at line:
-------------------------------------------------------
*
Could you please let me know what could be the problem..?
You've broken the format of the .rtp file used in ffG53a6. Use the
"diff" tool to compare the "before" and "after" versions. Be sure you
are using unix-style line endings.
Mark
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