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<br>Rasoul<br><br><div class="gmail_quote">On Thu, Jan 28, 2010 at 1:43 PM, Emanuel Peter <span dir="ltr"><<a href="mailto:Emanuel.Peter@chemie.uni-regensburg.de">Emanuel.Peter@chemie.uni-regensburg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Gromacs Users,<br>
<br>
I have performed the Martini Coarse Graining procedure for the<br>
simulation of two protein domains by using the two scripts atom2cg.awk<br>
and <a href="http://seq2itp.pl" target="_blank">seq2itp.pl</a>. Then I was able to perform my simulation of my coarse<br>
grained system. My problem is now to convert my final cg structure into<br>
an all atom structure. For this purpose I tried to use the tool g_fg2cg<br>
with the inputs containing my fine grained topology ,the coarse grained<br>
topology and my coarse grained structure file. But obviously all<br>
attempts to apply that tool ended up in a segmentation fault message. I<br>
also tried to convert my all atom structure into a cg structure which<br>
ended up with the same segmentation fault message. Could you give me<br>
some advice on that problem? Here is my screen output:<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-pfg LOV1_LOV2.pdb.top Input Topology file<br>
-pcg martini_v2.0_example.top Input, Opt! Topology file<br>
-c lov1lov2_42ns_27.1.pdb Input Generic trajectory: xtc trr<br>
trj gro<br>
g96 pdb<br>
-o out.gro Output Generic structure: gro g96 pdb xml<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-nice int 0 Set the nicelevel<br>
-n int 0 1: fg2cg transformation, 0: cg2fg<br>
transformation<br>
-wat int 0 1: rewrites FG_CG water to true fg water;<br>
-rad real 0.3 A radius for random atom insertion;<br>
<br>
calling cpp...<br>
processing topology...<br>
Generated 279 of the 1225 non-bonded parameter combinations<br>
Excluding 3 bonded neighbours for Protein_A 1<br>
Excluding 3 bonded neighbours for Protein_B 1<br>
NOTE:<br>
System has non-zero total charge: -2.999998e+00<br>
<br>
# G96BONDS: 2738<br>
# G96ANGLES: 3994<br>
# PDIHS: 1465<br>
# IDIHS: 1328<br>
# LJ14: 4520<br>
calling cpp...<br>
processing topology...<br>
Generated 0 of the 465 non-bonded parameter combinations<br>
Excluding 1 bonded neighbours for Protein 1<br>
Excluding 1 bonded neighbours for ProteinB 1<br>
NOTE:<br>
System has non-zero total charge: -6.000000e+00<br>
<br>
<br>
Number of fg atoms 2696<br>
Number of cg atoms 571<br>
Reading frame 0 time 42000.004 1264673691<br>
Segmentation fault<br>
<br>
When I applied this tool on the ubiquitin example I had another problem,<br>
but I did it in the same way as before. Here is the screen output:<br>
<br>
Option Filename Type Description<br>
------------------------------------------------------------<br>
-pfg 1ubq.top Input Topology file<br>
-pcg out3.top Input, Opt! Topology file<br>
-c 1UBQ.gro Input Generic trajectory: xtc trr trj gro<br>
g96 pdb<br>
-o out.gro Output Generic structure: gro g96 pdb xml<br>
<br>
Option Type Value Description<br>
------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>
-nice int 0 Set the nicelevel<br>
-n int 1 1: fg2cg transformation, 0: cg2fg<br>
transformation<br>
-wat int 0 1: rewrites FG_CG water to true fg water;<br>
-rad real 0.3 A radius for random atom insertion;<br>
<br>
calling cpp...<br>
processing topology...<br>
Generated 279 of the 1225 non-bonded parameter combinations<br>
Excluding 3 bonded neighbours for Protein_A 1<br>
Excluding 2 bonded neighbours for SOL 58<br>
# G96BONDS: 766<br>
# G96ANGLES: 1107<br>
# PDIHS: 428<br>
# IDIHS: 334<br>
# LJ14: 1304<br>
# SETTLE: 58<br>
calling cpp...<br>
cpp: out3.top: Datei oder Verzeichnis nicht gefunden<br>
cpp: warning: '-x c' after last input file has no effect<br>
cpp: no input files<br>
cpp exit code: 256<br>
Tried to execute: 'cpp<br>
-I/pc50417/pee18323/REVERSE_trans_gromacs/agromacs-reverse/share/top<br>
out3.top > grompp605Sk3'<br>
The 'cpp' command is defined in the .mdp file<br>
processing topology...<br>
<br>
Number of fg atoms 934<br>
Number of cg atoms 0<br>
Reading frames from gro file 'UBIQUITIN', 934 atoms.<br>
Reading frame 0 time 0.000 out.xtc<br>
Last frame 0 time 0.000<br>
<br>
Back Off! I just backed up out.gro to ./#out.gro.2#<br>
<br>
Cg structure computed !<br>
<br>
In that case out.gro did not contain any atoms.<br>
<br>
Thanks for any suggestions!<br>
<br>
Best regards,<br>
<br>
Emanuel Peter<br>
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</font></blockquote></div><br>