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On 24/01/2011 11:53 PM, udaya kiran wrote:
<blockquote
cite="mid:AANLkTinS0kYkOfnREV4GQdomvQWd+h1=qKAtGq4PLECm@mail.gmail.com"
type="cite">Dear GROMACS users,<br>
<br>
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.<br>
<br>
<br>
Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat<br>
<br>
Select the Force Field:<br>
0: GROMOS96 43a1 force field <br>
1: GROMOS96 43a2 force field (improved alkane dihedrals)<br>
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) <br>
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) <br>
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>
6: [DEPRECATED] Gromacs force field (see manual)<br>
7: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>
8: Encad all-atom force field, using scaled-down vacuum charges<br>
9: Encad all-atom force field, using full solvent charges <br>
4<br>
Opening library file ffG53a6.rtp<br>
Opening library file aminoacids.dat<br>
Opening library file aminoacids.dat<br>
WARNING: masses will be determined based on residue and atom
names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file atommass.dat<br>
Entries in atommass.dat: 178<br>
WARNING: vdwradii will be determined based on residue and atom
names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file vdwradii.dat<br>
Entries in vdwradii.dat: 28<br>
Opening library file dgsolv.dat<br>
Entries in dgsolv.dat: 7<br>
Opening library file electroneg.dat<br>
Entries in electroneg.dat: 71<br>
Opening library file elements.dat<br>
Entries in elements.dat: 218<br>
Reading 16L6_6S17_start.pdb...<br>
WARNING: all CONECT records are ignored<br>
Read '6S17 ', 39 atoms<br>
Opening library file
/usr/local/gromacs/share/gromacs/top/xlateat.dat<br>
26 out of 26 lines of xlateat.dat converted succesfully<br>
Analyzing pdb file<br>
There are 1 chains and 0 blocks of water and 6 residues with 39
atoms<br>
<br>
chain #res #atoms<br>
1 ' ' 6 39 <br>
<br>
All occupancies are one<br>
Opening library file ffG53a6.atp<br>
Atomtype 1<br>
Reading residue database... (ffG53a6)<br>
Opening library file ffG53a6.rtp<br>
Using default: not generating all possible dihedrals<br>
Using default: excluding 3 bonded neighbors<br>
Using default: generating 1,4 H--H interactions<br>
Using default: removing impropers on same bond as a proper<br>
<br>
<b>-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0.5<br>
Source code file: resall.c, line: 321<br>
<br>
Fatal error:<br>
in .rtp file at line:<br>
<br>
<br>
-------------------------------------------------------<br>
</b><br>
<br>
Could you please let me know what could be the problem..?<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
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