[gmx-users] compatibility of MOPAC charges with GROMACS ?
Dear all I'm trying to assemble a topology entry for S-nitrosocysteine. Searching through the examples in the PDB revealed quite a spread of bond lengths and angles - the N=O bond ranges from 1.2 to 1.47A, for example. To get more rigorously derived figures, and to calculate charges, I thought of using MOPAC http://www.openmopac.net/index.html I imagine that the bond lengths and angles from MOPAC will be reliable. My question is really how compatible the charges are with the GROMACS topologies? Would you have any qualms about mixing and matching? Surely MOPAC's estimates must be better than human guesstimates or, despite its general wonderful usefulness, PRODRG's estimates? Are there other programs for this? Any thoughts welcome Regards Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topology for nitrosylated cysteine?
Dear all Does anybody, by any chance, have a Gromacs topology file for a nitrosylated cysteine residue? If not, is anybody aware of information for this residue in other program packages, or will PRODRG be my best bet? Thanks in advance Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs - amber trajectory conversion - resolution
Dear all Previously I (and others) have posted with issues regarding the conversion of gromacs trajectories (nm) to amber format (Angstrom). You can get g87 files form trjconv which are the same format as amber but in the wrong units. It turns out there is a simple way to do these conversions - use catDCD http://www.ks.uiuc.edu/Development/MDTools/catdcd/ also now integrated into VMD. The amber formats are crd crdbox (without and with box, respectively) Thanks to John Stone at VMD for this. Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS compilation problem
Dear all I'm trying to compile the latest GROMACS 3.3.1 on the latest Ubuntu Linux. Due to some fftw installation issue I used ./configure --with-fft=fftpack make make install All seemed to work fine, but any program I try to run now gives me a crash of this kind [EMAIL PROTECTED]: g_clustsize :-) G R O M A C S (-: *** stack smashing detected ***: g_clustsize terminated Aborted (core dumped) Can anyone help? Thanks Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] conversion of xtc to g87 (amber) format trajectory files/bounding box problem?
Hi everyone I'd like to convert my Gromacs trajectory to an Amber format for use with the CAVER program. Reading round, it seems that Amber is equivalent to the g87 format so I can use trjconv to produce the file. This all seems to work well (the file gets read in and processed) except for a problem with the bounding box. When caver works on a PDB file and generates its own box it comes out like this Grid: [63 82 76] BBox: (39.198000 6.232000 19.088000 ,89.027000 71.759000 79.758000 ) The box that gets read from the g87 trajectory looks like this Grid: [7 9 7] BBox: (3.307000 0.906000 1.856000 ,8.843000 7.67 7.336000 ) From other reading there seems to be a unit issue (A vs nm) in the Gromacs/Amber comparison. The two boxes above are quite close to 10-fold different in all dimensions. Is this the source of my problem? How can I work around this? Thanks in advance for your help Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS compilation problem
Hi Erik Thanks for the reply. Yes, I get this cc (GCC) 4.1.2 20060928 (prerelease) (Ubuntu 4.1.1-13ubuntu5) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Thanks Daniel On Mon, 2007-04-23 at 17:37 +0200, Erik Lindahl wrote: Hi Daniel, Could you run cc --version and post the result? Apparently some new Linux distributions are shipping with a buggy prerelease of gcc. Cheers, Erik On Apr 23, 2007, at 5:21 PM, Daniel Rigden wrote: Dear all I'm trying to compile the latest GROMACS 3.3.1 on the latest Ubuntu Linux. Due to some fftw installation issue I used ./configure --with-fft=fftpack make make install All seemed to work fine, but any program I try to run now gives me a crash of this kind [EMAIL PROTECTED]: g_clustsize :-) G R O M A C S (-: *** stack smashing detected ***: g_clustsize terminated Aborted (core dumped) Can anyone help? Thanks Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] published work on MD timescales/biological motions
Dear all This is a general MD question I'm afraid but I think this the quickest way to access an informed community. I remember seeing a while back an article that said that although MD simulations only extend to a timescale shorter than some biological motions, that these motions are typically quite well represented in the MD trajectories. I think extracting principal components/essential dynamics was in there somewhere. Can anyone remind me what the article was or point me to any other literature with which to answer a referee's point that a standard length simulation may not have been long enough to see some expected motions? Thanks Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
