Dear All,<br><br> 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 <br>
.the .top file and topol .top file is created but .gro file cant be created , the command line and output is like this-<br>[nitu@localhost mdtap]$ pdb2gmx -f rr1.pdb -p rr1.top -o rr1.gro<br> :-) G R O M A C S (-:<br>
<br> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon<br><br> :-) VERSION 4.0.3 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br>
:-) pdb2gmx (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f rr1.pdb Input Structure file: gro g96 pdb tpr tpb tpa<br>
-o rr1.gro Output Structure file: gro g96 pdb<br> -p rr1.top Output Topology file<br> -i posre.itp Output Include file for topology<br> -n clean.ndx Output, Opt. Index file<br>
-q clean.pdb Output, Opt. Structure file: gro g96 pdb<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>-[no]merge bool no Merge chains into one molecule definition<br>-ff string select Force field, interactive by default. Use -h for<br> information.<br>
-water enum spc Water model to use: with GROMOS we recommend SPC,<br> with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p<br> or f3c<br>-[no]inter bool no Set the next 8 options to interactive<br>
-[no]ss bool no Interactive SS bridge selection<br>-[no]ter bool no Interactive termini selection, iso charged<br>-[no]lys bool no Interactive Lysine selection, iso charged<br>-[no]arg bool no Interactive Arganine selection, iso charged<br>
-[no]asp bool no Interactive Aspartic Acid selection, iso charged<br>-[no]glu bool no Interactive Glutamic Acid selection, iso charged<br>-[no]gln bool no Interactive Glutamine selection, iso neutral<br>
-[no]his bool no Interactive Histidine selection, iso checking<br> H-bonds<br>-angle real 135 Minimum hydrogen-donor-acceptor angle for a<br> H-bond (degrees)<br>
-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)<br>-[no]una bool no Select aromatic rings with united CH atoms on<br> Phenylalanine, Tryptophane and Tyrosine<br>
-[no]ignh bool no Ignore hydrogen atoms that are in the pdb file<br>-[no]missing bool no Continue when atoms are missing, dangerous<br>-[no]v bool no Be slightly more verbose in messages<br>-posrefc real 1000 Force constant for position restraints<br>
-vsite enum none Convert atoms to virtual sites: none, hydrogens<br> or aromatics<br>-[no]heavyh bool no Make hydrogen atoms heavy<br>-[no]deuterate bool no Change the mass of hydrogens to 2 amu<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>1<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp<br>
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>Opening library file /usr/local/gromacs/share/gromacs/top/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 /usr/local/gromacs/share/gromacs/top/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 /usr/local/gromacs/share/gromacs/top/vdwradii.dat<br>Entries in vdwradii.dat: 28<br>Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat<br>
Entries in dgsolv.dat: 7<br>Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat<br>Entries in electroneg.dat: 71<br>Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat<br>Entries in elements.dat: 218<br>
Reading rr1.pdb...<br>Read 7778 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>Gave chain 1 chain identifier 'A'<br>
There are 2 chains and 0 blocks of water and 1000 residues with 7778 atoms<br><br> chain #res #atoms<br> 1 'A' 535 4129 <br> 2 'B' 465 3649 <br><br>All occupancies are one<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.atp<br>
Atomtype 1<br>Reading residue database... (ffG43a2)<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp<br>Residue 96<br>Sorting it all out...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.hdb<br>
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2-n.tdb<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2-c.tdb<br><br>Back Off! I just backed up rr1.top to ./#rr1.top.1#<br>Processing chain 1 'A' (4129 atoms, 535 residues)<br>
There are 793 donors and 782 acceptors<br>There are 1125 hydrogen bonds<br>Will use HISB for residue 54<br>Will use HISB for residue 56<br>Will use HISB for residue 58<br>Will use HISB for residue 297<br>Will use HISB for residue 373<br>
Will use HISA for residue 377<br>Will use HISA for residue 421<br>Will use HISB for residue 501<br>Will use HISB for residue 510<br>Will use HISB for residue 525<br>Checking for duplicate atoms....<br>Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat<br>
7 out of 7 lines of specbond.dat converted succesfully<br>Special Atom Distance matrix:<br> MET1 MET30 MET52 HISB54 HISB56 HISB58 MET84<br> SD5 SD237 SD399 NE2414 NE2431 NE2447 SD655<br>
MET30 SD237 2.142<br> MET52 SD399 3.719 3.391<br> HISB54 NE2414 4.637 4.052 1.298<br> HISB56 NE2431 4.239 3.979 0.590 1.165<br> HISB58 NE2447 4.646 4.190 1.275 0.284 1.053<br> MET84 SD655 5.754 5.220 2.140 2.170 1.713 2.135<br>
CYS114 SG894 2.411 3.578 2.551 3.301 2.817 3.173 4.458<br> MET119 SD929 2.058 3.681 3.171 4.176 3.473 4.061 4.965<br> MET128 SD997 3.027 4.810 4.011 4.900 4.191 4.735 5.617<br>
MET173 SD1349 7.038 6.386 3.774 3.973 3.455 3.974 1.861<br> MET219 SD1713 2.720 3.806 2.903 4.145 3.163 4.046 4.278<br> MET251 SD1947 1.861 2.949 2.658 3.856 3.059 3.800 4.392<br>
CYS287 SG2241 7.103 6.823 3.518 2.892 2.946 2.741 2.239<br> HISB297 NE22313 8.076 7.570 4.634 3.559 4.161 3.485 3.719<br> HISB373 NE22889 7.215 6.806 3.583 2.833 3.035 2.719 2.272<br>
HISA377 NE22930 7.515 7.083 3.870 3.120 3.323 3.015 2.453<br> MET408 SD3168 7.719 6.465 4.327 3.436 4.084 3.587 3.203<br> HISA421 NE23258 8.663 7.440 5.167 4.370 4.863 4.487 3.665<br>
CYS461 SG3547 8.510 7.894 4.893 3.927 4.397 3.878 3.542<br> HISB501 NE23865 9.371 8.660 5.699 5.235 5.217 5.211 3.621<br> HISB510 NE23935 10.036 9.574 6.370 5.672 5.814 5.582 4.604<br>
HISB525 NE24045 10.619 9.962 6.908 6.272 6.389 6.227 4.945<br> MET529 SD4078 10.874 10.283 7.181 6.606 6.651 6.547 5.186<br> CYS534 SG4116 10.297 9.934 6.679 6.204 6.116 6.097 4.758<br>
CYS114 MET119 MET128 MET173 MET219 MET251 CYS287<br> SG894 SD929 SD997 SD1349 SD1713 SD1947 SG2241<br> MET119 SD929 1.156<br> MET128 SD997 1.765 1.167<br> MET173 SD1349 6.026 6.300 6.950<br>
MET219 SD1713 2.221 1.503 2.241 5.268<br> MET251 SD1947 1.823 1.233 2.324 5.545 0.925<br> CYS287 SG2241 5.222 5.982 6.313 3.385 5.678 5.827<br> HISB297 NE22313 6.244 7.197 7.542 4.862 7.158 7.127 1.916<br>
HISB373 NE22889 5.412 6.205 6.592 3.401 5.913 6.007 0.456<br> HISA377 NE22930 5.718 6.501 6.880 3.427 6.183 6.293 0.624<br> MET408 SD3168 6.715 7.487 8.245 3.749 7.096 6.916 3.440<br>
HISA421 NE23258 7.599 8.320 9.039 3.716 7.805 7.722 3.724<br> CYS461 SG3547 6.770 7.635 8.033 4.311 7.399 7.432 1.889<br> HISB501 NE23865 7.907 8.468 8.944 2.985 7.733 7.973 3.159<br>
HISB510 NE23935 8.188 8.904 9.171 4.665 8.457 8.694 2.974<br> HISB525 NE24045 8.968 9.620 9.992 4.543 9.015 9.255 3.834<br> MET529 SD4078 9.189 9.805 10.138 4.686 9.164 9.451 4.076<br>
CYS534 SG4116 8.475 9.054 9.283 4.425 8.440 8.798 3.458<br> HISB297 HISB373 HISA377 MET408 HISA421 CYS461 HISB501<br> NE22313 NE22889 NE22930 SD3168 NE23258 SG3547 NE23865<br>
HISB373 NE22889 1.614<br> HISA377 NE22930 1.559 0.310<br> MET408 SD3168 3.188 3.029 3.017<br> HISA421 NE23258 3.499 3.323 3.212 1.123<br> CYS461 SG3547 1.031 1.528 1.308 2.803 2.809<br> HISB501 NE23865 3.780 3.012 2.773 3.480 2.771 2.805<br>
HISB510 NE23935 2.943 2.876 2.572 4.371 3.872 2.138 2.161<br> HISB525 NE24045 3.884 3.676 3.374 4.342 3.545 2.906 1.585<br> MET529 SD4078 4.260 3.969 3.670 4.815 4.021 3.310 1.797<br>
CYS534 SG4116 3.992 3.480 3.204 5.084 4.502 3.187 2.046<br> HISB510 HISB525 MET529<br> NE23935 NE24045 SD4078<br> HISB525 NE24045 1.350<br> MET529 SD4078 1.505 0.527<br>
CYS534 SG4116 1.271 1.483 1.219<br>N-terminus: NH3+<br>C-terminus: COO-<br>Now there are 535 residues with 5226 atoms<br>Chain time...<br><br>Back Off! I just backed up rr1_A.itp to ./#rr1_A.itp.1#<br>Making bonds...<br>
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br><br>WARNING: atom OH is missing in residue TYR 535 in the pdb file<br><br><br>WARNING: atom HH is missing in residue TYR 535 in the pdb file<br> You might need to add atom HH to the hydrogen database of residue TYR<br>
in the file ff???.hdb (see the manual)<br><br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.0.3<br>Source code file: pdb2top.c, line: 704<br><br>Fatal error:<br>There were 2 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing<br>
-------------------------------------------------------<br><br>"The World is a Friendly Place" (Magnapop)<br><br>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 <br>
<br><br>plese if possible than anybody help me.<br><br>Thank you very much for taking out of your time for my consideration.<br><br>Nitu Sharma<br>Structural Biology lab<br>School Of Life sciences<br>Jawaherlal Nehru University<br>
New Delhi, India<br>