Re: [gmx-users] editconf/genbox problem in Gromacs 4.0
Many thanks to Bert and Xavier. Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb use gro files for output and it works. The box size is not written in the pdb file, although it used to be. Yes, it works, but I'm using .pdb instead of .gro format to support chain identifiers since my system is composed by 3 protein chains. So I will wait for the new 4.0.1 release. Caterina ___ 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] editconf/genbox problem in Gromacs 4.0
Right! Thanks again Berk. Caterina 2008/11/7 Berk Hess [EMAIL PROTECTED]: Hi, For the moment you can use editconf of 3.3 or copy a cryst1 entry (one of the first lines) from another pdb file into you pdb input file, editconf will then write the correct box in the output pdb. Berk Date: Fri, 7 Nov 2008 12:13:55 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] editconf/genbox problem in Gromacs 4.0 Many thanks to Bert and Xavier. Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb use gro files for output and it works. The box size is not written in the pdb file, although it used to be. Yes, it works, but I'm using .pdb instead of .gro format to support chain identifiers since my system is composed by 3 protein chains. So I will wait for the new 4.0.1 release. Caterina ___ gmx-users mailing list gmx-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 Express yourself instantly with MSN Messenger! MSN Messenger ___ 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
[gmx-users] editconf/genbox problem in Gromacs 4.0
Dear gmx-users, I have encountered a similar editconf/genbox problem posted by Matt Danielson on 14 October: I 'm using Gromacs 4.0 (installed on MacOS). 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb The output from editconf does not report errors, but I noted that the volume of the box is 0! --- output message--- WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type 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 Entries in vdwradii.dat: 28 Entries in dgsolv.dat: 7 Entries in electroneg.dat: 71 Entries in elements.dat: 218 Read 16824 atoms Volume: 0 nm^3, corresponds to roughly 0 electrons - 2. genbox_d -cp my_protein_box.pdb -cs spc216.gro -o my_protein_wat.pdb -p my_protein.top The output from genbox_d reports the following error: --- Program genbox, VERSION 4.0 Source code file: gmx_genbox.c, line: 744 Fatal error: Undefined solute box. Create one with editconf or give explicit -box command line option --- I have performed the same commands on another machine (Linux) running version 3.3 and I produced with success a nice solvent box. Suggestions? Thanks, Caterina -- Caterina Arcangeli ENEA, Dept. Physics (FIM-CAMO) C.R. Casaccia, SP 026 Via Anguillarese 301 - 00123 Roma ___ 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] ED analysis: help on cosine content and overlap of the fluctuatio
I thank Ran and Berk for useful and critical discussion. Caterina I agree with Ran. But on your quesion of inconsistency. It seems like your essential subspace (the space spanned by the first 10 eigenvectors) has converged. But this does not say much about the convergence of the first few eigenvectors in this subspace. From the cosine content one can clearly say that M1 is not converged. Since M2 is a subset of M1 it is also not converged. So for proper sampling of global conformations you would need to simulate several orders of magnitude longer, as one would expect for a 253 residue protein. If you need this for what you are interested in is another question. Berk. From: Ran Friedman [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] ED analysis: help on cosine content and overlap ofthefluctuations Date: Fri, 13 Apr 2007 13:44:19 +0200 Dear Caterina, GMX users, It's very difficult to decide whether a simulation converged, at least for macromolecules. There are a lot of studies in the literature about it, but there's no concrete answer. I'd try to ask when the results can be useful, and not when the simulation (or PC) converged - and that depends on your system and what you are trying to model. One hint is that a PC with a high cosine content is probably not going to be very useful if you try to simulate any kind of structural transitions. Ran. Caterina Arcangeli wrote: Dear all, I performed essential dynamics (ED) analysis on my protein (253 amino acids). The simulation (10ns) achieves stability in the RMSD after 6.0ns, but a convergence analysis based on cluster analysis (as described by Daura, 1999) indicates that the conformational sampling reaches a stable value only for the last 1.0ns. So, I've performed ED on both 6-10 ns (M1) and 9-10ns (M2) time interval using g_covar. To check if the principal modes are well defined, I've calulated the ovelap of the sampling between the first and second half of the trajectories (I've splitted M1 and M2 into two halves) and the cosine content of the first eigenvectors: - the normalized overlaps are 0.499 (M1) and 0.434 (M2); - the subspace overlaps (rmsip) for the first 10 eigenvectors are 0.748 (M1) and 0.686 (M2); - the cosine content of the first eigenvectors is 0.828 (pc1) for M1 and 0.125 (pc1) for M2. So, apparently, the two method are inconsistent: a higher rmsip value is observed for M1 (according to Amadei, a rmsip value 0.7 shows a reasonable convergence) wheras the lower cosine content is obtained for M2 (according to Hess, a value 0.5 indicates jumping between clusters and not a merely random diffusion). My questions are: which time window better describe the dynamics of my protein? From where come out this inconsistency? What I'm wrong? Thank to all. Caterina P.S. I aware that 10 ns are in general insufficient to describe the thermodynamics of a protein but I want just to have an idea of some structural properties of my protein. ___ 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 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ 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 _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ 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 -- Caterina Arcangeli ENEA
[gmx-users] ED analysis: help on cosine content and overlap of the fluctuations
Dear all, I performed essential dynamics (ED) analysis on my protein (253 amino acids). The simulation (10ns) achieves stability in the RMSD after 6.0ns, but a convergence analysis based on cluster analysis (as described by Daura, 1999) indicates that the conformational sampling reaches a stable value only for the last 1.0ns. So, I've performed ED on both 6-10 ns (M1) and 9-10ns (M2) time interval using g_covar. To check if the principal modes are well defined, I've calulated the ovelap of the sampling between the first and second half of the trajectories (I've splitted M1 and M2 into two halves) and the cosine content of the first eigenvectors: - the normalized overlaps are 0.499 (M1) and 0.434 (M2); - the subspace overlaps (rmsip) for the first 10 eigenvectors are 0.748 (M1) and 0.686 (M2); - the cosine content of the first eigenvectors is 0.828 (pc1) for M1 and 0.125 (pc1) for M2. So, apparently, the two method are inconsistent: a higher rmsip value is observed for M1 (according to Amadei, a rmsip value 0.7 shows a reasonable convergence) wheras the lower cosine content is obtained for M2 (according to Hess, a value 0.5 indicates jumping between clusters and not a merely random diffusion). My questions are: which time window better describe the dynamics of my protein? From where come out this inconsistency? What I'm wrong? Thank to all. Caterina P.S. I aware that 10 ns are in general insufficient to describe the thermodynamics of a protein but I want just to have an idea of some structural properties of my protein. ___ gmx-users mailing list[EMAIL PROTECTED] 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] help on g_hbond -contact
Dear all, I would like to compute the residue contacts within the protein. In particular I want to obtain the pair residues forming contacts with a distance cut-off of 0.4 nm. I used g_hbond -contact: g_hbond_d -f my_protein.trr -s my_protein.tpr -n my_protein.ndx -nomerge -contact -r 0.4 However I obtained the following message: Fatal error: Donor 2419 does not have hydrogen -12344 (a = 2412) The same command without -contact produces fine results, i.e. the number of hbonds, without errors. I'm using GROMACS 3.3 version. Suggestions? Thanks to all. -- Caterina Arcangeli ENEA, Computing and Modelling Unit (CAMO) Casaccia Research Center - Post Bag 026 Via Anguillarese 301 - 00060 Roma phone +39 06.3048.6898 fax +39 06.3048.6860 http://www.enea.it ___ 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
Re: [gmx-users] help on g_hbond -contact
Thanks to Tsjerk and Erik for their prompt replies. I've looked at g_saltbr and it seems to be appropriate for my requirements. Caterina Erik Marklund wrote: Well... g_hbond works, surprisingly, for non-hydrogen bonds with the -contact flag. However, that part of the g_hbond code was not really functional in gromacs 3.3. I suggest doing what Tsjerk suggested, or trying g_hbond -contact with a newer version of gromacs. g_saltbr may also provide useful insight about intermolecular contacts. /Erik 26 feb 2007 kl. 20.09 skrev Tsjerk Wassenaar: Hi Caterina, g_hbond is, surprisingly, for h-bonds. If you want contacts, try g_mindist. Cheers, Tsjerk On 2/26/07, Caterina Arcangeli [EMAIL PROTECTED] wrote: Dear all, I would like to compute the residue contacts within the protein. In particular I want to obtain the pair residues forming contacts with a distance cut-off of 0.4 nm. I used g_hbond -contact: g_hbond_d -f my_protein.trr -s my_protein.tpr -n my_protein.ndx -nomerge -contact -r 0.4 However I obtained the following message: Fatal error: Donor 2419 does not have hydrogen -12344 (a = 2412) The same command without -contact produces fine results, i.e. the number of hbonds, without errors. I'm using GROMACS 3.3 version. Suggestions? Thanks to all. -- Caterina Arcangeli ENEA, Computing and Modelling Unit (CAMO) Casaccia Research Center - Post Bag 026 Via Anguillarese 301 - 00060 Roma phone +39 06.3048.6898 fax +39 06.3048.6860 http://www.enea.it ___ 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 --Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 [EMAIL PROTECTED]http://xray.bmc.uu.se/molbiophys ___ 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 thewww 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 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] About g_cluster
Brigo et al. Biophys J. (2005) 88:3072 Smith et al. Proteins (2002) 48:487 Ciao Caterina Cesar Araujo ha scritto: Hi, Can anybody give some reference about a good explanation on how to use g_cluster in order to analyze a set of simulations on complexes differing one each other in their starting point conformation? Thanks in adavance, César.- --- Cesar Araujo, Lic. of Chemistry Research Center for Molecular Endocrinology P.O. Box 5000, FIN-90014 University of Oulu Finland phone: +358 8 3155632 e-mail: [EMAIL PROTECTED] ___ 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 ___ 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
Re: [gmx-users] (no subject)
Hi, using the command: trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -o nchnp3_15pep.trr -settime the program will ask you the start time of each file. Try putting 5001 for the first file and c (continue) for the second file. It should be work. Ciao Caterina Mark Abraham wrote: sharada wrote: Hello gmx_users, I wish you a very happy and prosperous new year 2007. I have a very fundamental question in trjcat usage. I have two *.trr files of 5ns and 10 ns runs . I would like to concanate the two and make a 15ns trr file. How to give the command so that the starting time of the 10ns file should be 5001ps and not 0ps and end time is 15000ps and not 1 ps. May this is a trivial question. Kindly help. I have tried using the following command : trjcat -f nchnp3_5npep.trr nchnp3_10pep.trr -settime -o nchnp3_15pep.trr -b 0.00 -e 15000 It's just like the command line utility cat... it will do a straight concatenation. trjcat -f 5n.trr 10n.trr -o 15n.trr should do what you want. Check using gmxdump , of course Mark ___ 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 -- Caterina Arcangeli ENEA, Computing and Modelling Unit (CAMO) Casaccia Research Center - Post Bag 026 Via Anguillarese 301 - 00060 Roma phone +39 06.3048.6898 fax +39 06.3048.6860 http://www.enea.it ___ 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
[gmx-users] help on g_cluster transitions
Hi all, I'm doing cluster analysis of my protein simulation. I use gromos method on the Ca atoms and I obtain 10 clusters. Is not clear to me the (biological) meaning of transition between clusters. 1. Are transitions occurring among different conformational states? 2. What does means if one found several clusters-transitions: maybe that the simulation is not stable? Thank to all. Caterina P.S. Here is the .log file I've obtained: -- Using gromos method for clustering Using RMSD cutoff 0.1 nm The RMSD ranges from 0.046404 to 0.181787 nm Average RMSD is 0.117163 Number of structures for matrix 561 Energy of the matrix is 23.5304 nm Found 10 clusters Writing average structure for each cluster to cluster/pdb_average/F8M47_cluster.pdb Writing all structures for clusters with more than 1 structures to cluster/pdb_average/F8M47_cluster%02d.pdb Counted 106 transitions in total, max 17 between two specific clusters cl. | #st rmsd | middle rmsd | cluster members 1 | 264 .103 | 2832 .090 | 2302 2324 2370 2372 2374 2380 2 | 128 .097 | 2082 .086 | 2020 2022 2024 2026 2028 2030 3 | 49 .099 | 2368 .090 | 2262 2268 2274 2276 2282 2298 4 | 48 .095 | 2650 .085 | 2514 2516 2518 2520 2526 2534 5 | 34 .088 | 3086 .077 | 3028 3032 3040 3048 3050 3052 6 | 18 .094 | 2260 .085 | 2232 2236 2238 2240 2242 2244 7 | 13 .092 | 2012 .081 | 2000 2002 2004 2006 2008 2010 8 | 3 .090 | 2484 .086 | 2460 2484 2524 9 | 3 .087 | 3110 .079 | 2914 3108 3110 10 | 1 | 2332 | 2332 ___ 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
[gmx-users] help on g_cluster transitions
Hi all, I'm doing cluster analysis of my protein simulation. I use gromos method on the Ca atoms and I obtain 10 clusters. Is not clear to me the (biological) meaning of transition between clusters. 1. Are transitions occurring among different conformational states? 2. What does means if one found several clusters-transitions: maybe that the simulation is not stable? Thank to all. Caterina P.S. Here is the .log file I've obtained: -- Using gromos method for clustering Using RMSD cutoff 0.1 nm The RMSD ranges from 0.046404 to 0.181787 nm Average RMSD is 0.117163 Number of structures for matrix 561 Energy of the matrix is 23.5304 nm Found 10 clusters Writing average structure for each cluster to cluster/pdb_average/F8M47_cluster.pdb Writing all structures for clusters with more than 1 structures to cluster/pdb_average/F8M47_cluster%02d.pdb Counted 106 transitions in total, max 17 between two specific clusters cl. | #st rmsd | middle rmsd | cluster members 1 | 264 .103 | 2832 .090 | 2302 2324 2370 2372 2374 2380 2 | 128 .097 | 2082 .086 | 2020 2022 2024 2026 2028 2030 3 | 49 .099 | 2368 .090 | 2262 2268 2274 2276 2282 2298 4 | 48 .095 | 2650 .085 | 2514 2516 2518 2520 2526 2534 5 | 34 .088 | 3086 .077 | 3028 3032 3040 3048 3050 3052 6 | 18 .094 | 2260 .085 | 2232 2236 2238 2240 2242 22447 | 13 .092 | 2012 .081 | 2000 2002 2004 2006 2008 2010 8 | 3 .090 | 2484 .086 | 2460 2484 2524 9 | 3 .087 | 3110 .079 | 2914 3108 3110 10 | 1 | 2332 | 2332 ___ 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
