Vitaly Chaban wrote:
Amanda,
X2TOP is a somewhat enigmatic tool. You are never sure when it why it
works or refuses to generate a topology...
Try to start with PDB file instead of GRO. Try to use -"pbc" keyword.
Try to add new lines to N2T database corresponding to all atoms of
your molecule.
The -pbc option is broken in the 4.0.x series and will cause the program to hang
in every case I've seen it invoked. You must use -nopbc to get the program to
complete.
-Justin
Good luck,
Vitaly
I have tried to convert this file to a top file but this is the error message I
get:
Opening library file /usr/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 /usr/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 /usr/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Looking whether force field files exist
Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
Opening library file /usr/share/gromacs/top/ffoplsaa.n2t
Opening library file /usr/share/gromacs/top/ffoplsaa.n2t
There are 23 name to type translations
Generating bonds from distances...
atom 48
Can not find forcefield for atom C-4 with 2 bonds
-------------------------------------------------------
Program x2top, VERSION 4.0.7
Source code file: ../../../../src/kernel/x2top.c, line: 207
Fatal error:
Could only find a forcefield type for 47 out of 48 atoms
-------------------------------------------------------
"Throwing the Baby Away With the SPC" (S. Hayward)
I have tried to adjust the coordinates within the gro file but it still shows
the same message. Someone please give me some proper instruction in the
conversion of a .gro file to a .top file. Thank you!
Sincerely,
Amanda M. Watkins
SBC 2012
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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