[gmx-users] problem in creating .gro file
nitu sharma
sharmanitu35 at gmail.com
Mon Mar 2 13:22:58 CET 2009
Dear All,
I have successfully installed gromacs -4.0.3 on my
linux fedora core-8 i686 32 bit computer but I was not able to source the
GMXRC script because in my system only "bash shell" is active so I want to
know is C-shell must needed to run gromacs successfully? Because I am
facing one problem i.e .gro file doesn't created when i put the command to
create .gro and .top file
.the .top file and topol .top file is created but .gro file cant be created
, the command line and output is like this-
[nitu at localhost mdtap]$ pdb2gmx -f rr1.pdb -p rr1.top -o rr1.gro
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.0.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) pdb2gmx (-:
Option Filename Type Description
------------------------------------------------------------
-f rr1.pdb Input Structure file: gro g96 pdb tpr tpb tpa
-o rr1.gro Output Structure file: gro g96 pdb
-p rr1.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]merge bool no Merge chains into one molecule definition
-ff string select Force field, interactive by default. Use -h for
information.
-water enum spc Water model to use: with GROMOS we recommend
SPC,
with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p
or f3c
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, iso charged
-[no]lys bool no Interactive Lysine selection, iso charged
-[no]arg bool no Interactive Arganine selection, iso charged
-[no]asp bool no Interactive Aspartic Acid selection, iso charged
-[no]glu bool no Interactive Glutamic Acid selection, iso charged
-[no]gln bool no Interactive Glutamine selection, iso neutral
-[no]his bool no Interactive Histidine selection, iso checking
H-bonds
-angle real 135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-dist real 0.3 Maximum donor-acceptor distance for a H-bond
(nm)
-[no]una bool no Select aromatic rings with united CH atoms on
Phenylalanine, Tryptophane and Tyrosine
-[no]ignh bool no Ignore hydrogen atoms that are in the pdb file
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real 1000 Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu
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
1
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/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/local/gromacs/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/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading rr1.pdb...
Read 7778 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
Gave chain 1 chain identifier 'A'
There are 2 chains and 0 blocks of water and 1000 residues with 7778 atoms
chain #res #atoms
1 'A' 535 4129
2 'B' 465 3649
All occupancies are one
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.atp
Atomtype 1
Reading residue database... (ffG43a2)
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.hdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2-n.tdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2-c.tdb
Back Off! I just backed up rr1.top to ./#rr1.top.1#
Processing chain 1 'A' (4129 atoms, 535 residues)
There are 793 donors and 782 acceptors
There are 1125 hydrogen bonds
Will use HISB for residue 54
Will use HISB for residue 56
Will use HISB for residue 58
Will use HISB for residue 297
Will use HISB for residue 373
Will use HISA for residue 377
Will use HISA for residue 421
Will use HISB for residue 501
Will use HISB for residue 510
Will use HISB for residue 525
Checking for duplicate atoms....
Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat
7 out of 7 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
MET1 MET30 MET52 HISB54 HISB56 HISB58 MET84
SD5 SD237 SD399 NE2414 NE2431 NE2447 SD655
MET30 SD237 2.142
MET52 SD399 3.719 3.391
HISB54 NE2414 4.637 4.052 1.298
HISB56 NE2431 4.239 3.979 0.590 1.165
HISB58 NE2447 4.646 4.190 1.275 0.284 1.053
MET84 SD655 5.754 5.220 2.140 2.170 1.713 2.135
CYS114 SG894 2.411 3.578 2.551 3.301 2.817 3.173 4.458
MET119 SD929 2.058 3.681 3.171 4.176 3.473 4.061 4.965
MET128 SD997 3.027 4.810 4.011 4.900 4.191 4.735 5.617
MET173 SD1349 7.038 6.386 3.774 3.973 3.455 3.974 1.861
MET219 SD1713 2.720 3.806 2.903 4.145 3.163 4.046 4.278
MET251 SD1947 1.861 2.949 2.658 3.856 3.059 3.800 4.392
CYS287 SG2241 7.103 6.823 3.518 2.892 2.946 2.741 2.239
HISB297 NE22313 8.076 7.570 4.634 3.559 4.161 3.485 3.719
HISB373 NE22889 7.215 6.806 3.583 2.833 3.035 2.719 2.272
HISA377 NE22930 7.515 7.083 3.870 3.120 3.323 3.015 2.453
MET408 SD3168 7.719 6.465 4.327 3.436 4.084 3.587 3.203
HISA421 NE23258 8.663 7.440 5.167 4.370 4.863 4.487 3.665
CYS461 SG3547 8.510 7.894 4.893 3.927 4.397 3.878 3.542
HISB501 NE23865 9.371 8.660 5.699 5.235 5.217 5.211 3.621
HISB510 NE23935 10.036 9.574 6.370 5.672 5.814 5.582 4.604
HISB525 NE24045 10.619 9.962 6.908 6.272 6.389 6.227 4.945
MET529 SD4078 10.874 10.283 7.181 6.606 6.651 6.547 5.186
CYS534 SG4116 10.297 9.934 6.679 6.204 6.116 6.097 4.758
CYS114 MET119 MET128 MET173 MET219 MET251 CYS287
SG894 SD929 SD997 SD1349 SD1713 SD1947 SG2241
MET119 SD929 1.156
MET128 SD997 1.765 1.167
MET173 SD1349 6.026 6.300 6.950
MET219 SD1713 2.221 1.503 2.241 5.268
MET251 SD1947 1.823 1.233 2.324 5.545 0.925
CYS287 SG2241 5.222 5.982 6.313 3.385 5.678 5.827
HISB297 NE22313 6.244 7.197 7.542 4.862 7.158 7.127 1.916
HISB373 NE22889 5.412 6.205 6.592 3.401 5.913 6.007 0.456
HISA377 NE22930 5.718 6.501 6.880 3.427 6.183 6.293 0.624
MET408 SD3168 6.715 7.487 8.245 3.749 7.096 6.916 3.440
HISA421 NE23258 7.599 8.320 9.039 3.716 7.805 7.722 3.724
CYS461 SG3547 6.770 7.635 8.033 4.311 7.399 7.432 1.889
HISB501 NE23865 7.907 8.468 8.944 2.985 7.733 7.973 3.159
HISB510 NE23935 8.188 8.904 9.171 4.665 8.457 8.694 2.974
HISB525 NE24045 8.968 9.620 9.992 4.543 9.015 9.255 3.834
MET529 SD4078 9.189 9.805 10.138 4.686 9.164 9.451 4.076
CYS534 SG4116 8.475 9.054 9.283 4.425 8.440 8.798 3.458
HISB297 HISB373 HISA377 MET408 HISA421 CYS461 HISB501
NE22313 NE22889 NE22930 SD3168 NE23258 SG3547 NE23865
HISB373 NE22889 1.614
HISA377 NE22930 1.559 0.310
MET408 SD3168 3.188 3.029 3.017
HISA421 NE23258 3.499 3.323 3.212 1.123
CYS461 SG3547 1.031 1.528 1.308 2.803 2.809
HISB501 NE23865 3.780 3.012 2.773 3.480 2.771 2.805
HISB510 NE23935 2.943 2.876 2.572 4.371 3.872 2.138 2.161
HISB525 NE24045 3.884 3.676 3.374 4.342 3.545 2.906 1.585
MET529 SD4078 4.260 3.969 3.670 4.815 4.021 3.310 1.797
CYS534 SG4116 3.992 3.480 3.204 5.084 4.502 3.187 2.046
HISB510 HISB525 MET529
NE23935 NE24045 SD4078
HISB525 NE24045 1.350
MET529 SD4078 1.505 0.527
CYS534 SG4116 1.271 1.483 1.219
N-terminus: NH3+
C-terminus: COO-
Now there are 535 residues with 5226 atoms
Chain time...
Back Off! I just backed up rr1_A.itp to ./#rr1_A.itp.1#
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: atom OH is missing in residue TYR 535 in the pdb file
WARNING: atom HH is missing in residue TYR 535 in the pdb file
You might need to add atom HH to the hydrogen database of residue
TYR
in the file ff???.hdb (see the manual)
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.3
Source code file: pdb2top.c, line: 704
Fatal error:
There were 2 missing atoms in molecule Protein_A, if you want to use this
incomplete topology anyhow, use the option -missing
-------------------------------------------------------
"The World is a Friendly Place" (Magnapop)
How can I use missing option and can be able to create .gro file could
anybody help me in doing my work becoz I just started working with gromacs
so i am facing these type of problems
plese if possible than anybody help me.
Thank you very much for taking out of your time for my consideration.
Nitu Sharma
Structural Biology lab
School Of Life sciences
Jawaherlal Nehru University
New Delhi, India
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