Dear all, I am trying to study the MD of a Carbon Nanotube interacting with
some polymers. and I have some problems in forming the topology files. I have
actually two questions and I hope you can help me in that.
(1) In an attempt to form the topology files of CNTs and graphene (using
x2top), i have found on the internet scripts (by Andrea Minoia I guess). These
constitute of adding .nt2, .rtp. and .itp files to the
/Gromacs/share/Gromacs/top directory (namely ffcntoplsaa.nt2, ffcntoplsaa.rtp
and ffcntoplsaa.itp) and adding a line in the FF.dat file. I have done that and
tried to execute x2top and I got the error:
"......Entries in elements.dat: 218Looking whether force field files
existOpening library file
/cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening library
file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening
library file
/cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 name
to type translationsGenerating bonds from distances...Segmentation fault (core
dumped)"
Can anyone please tell me the source of this error and how to fix it?
(2) I will definitely need a top file for the polymers I will also be
solvating. But I also have problems because the pdb file contains a LIG residue
unrecognizable by Gromacs. I have asked this question before and I was advised
to change some files accordingly but to be honest I am not really professional
in that; I have asked someone who had a problem in the past but he did not know
all the details because he ended up not using the modified force fields after
all. Can anyone give me in details how to incorporate the residue "LIG" within
the force field or let me know whom I can consult...A part of the pdb file with
the residue LIG is:
"COMPND UNNAMEDAUTHOR GENERATED BY OPEN BABEL 2.3.1HETATM 1 C LIG
1 1.481 -1.276 -0.621 1.00 0.00 CHETATM 2 C LIG
1 2.216 -2.370 -1.040 1.00 0.00 CHETATM 3 S LIG 1
3.770 -2.409 -0.306 1.00 0.00 SHETATM 4 C LIG 1
3.456 -0.998 0.609 1.00 0.00 CHETATM 5 C LIG 1
2.207 -0.479 0.313 1.00 0.00 CHETATM 6 C LIG 1
5.156 0.676 1.386 1.00 0.00 CHETATM 7 C LIG 1
4.423 -0.491 1.600 1.00 0.00 CHETATM 8 C LIG 1
4.550 -1.119 2.847 1.00 0.00 CHETATM 9 C LIG 1
5.256 -0.503 3.905 1.00 0.00 CHETATM 10 C LIG 1
6.107 0.592 3.667 1.00 0.00 CHETATM 11 C LIG 1
6.008 1.181 2.393 1.00 0.00 CHETATM 12 S LIG 1
7.457 2.548 5.198 1.00 0.00 SHETATM 13 C LIG 1
7.220 0.945 4.621 1.00 0.00 ..."
I am really thankful
Elie --
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