Re: [gmx-users] Arbitrary S-S bonds
What kind of parameters are you using? Gromacs? Amber? I was told you can check for previous calculations done for S-S bonds in published papers, find its constants, bond length, and all and add them to the bonds' parameter file. Then generate a .gro and a .top. It could work. Just make sure you convert to the appropiate units. Good luck. ==Original message text=== On Tue, 25 Jul 2006 13:59:14 EDT "Cesar Araujo" wrote: Hi, Can anybody tell me how can I generate arbitrary S-S bonds with gromacs? The problem is that I have a protein and I want to specify some S-S bond between two cysteine residues but they are not an options given by pdb2gmx -ss. Should I touch topology file by hand? Why pdb2gmx do not recognizes automatically SSBOND records in pdb files? Regards, César.-===End of original message text=== ___ 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] Fw: grompp lib/cpp problem
==Original message text===From: [EMAIL PROTECTED]Date: Mon, 24 Jul 2006 20:00:57 EDTSubject: Re: [gmx-users] REST variant of REMDHi i'm getting this line from a nohup.out file. I am trying to run grompp in a loop for several files and the script is not working. What does this mean?creating statusfile for 1 node...calling /lib/cpp...cpp exit code: 256Tried to execute: '/lib/cpp -I../top-I/home/diana/software/gromacs-3.3/share/gromacs/top 1bq8zn.top >gromppgr1Igp'The '/lib/cpp' command is defined in the .mdp fileprocessing topology...turning H bonds into constraints...___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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===End of original message text=== ___ 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] REST variant of REMD
Hi i'm getting this line from a nohup.out file. I am trying to run grompp in a loop for several files and the script is not working. What does this mean? creating statusfile for 1 node... calling /lib/cpp... cpp exit code: 256 Tried to execute: '/lib/cpp -I../top -I/home/diana/software/gromacs-3.3/share/gromacs/top 1bq8zn.top > gromppgr1Igp' The '/lib/cpp' command is defined in the .mdp file processing topology... turning H bonds into constraints... ___ 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] editconf -d
==Original message text===On Wed, 19 Jul 2006 10:18:30 EDT Isabella Daidone wrote:-d is not for centering. -d is the distance of the protein from the walls of the box. Hi,when using editconf -d with gromacs version 3.3, it seems that the protein is not at the center but at the corner of the box.In gromacs version 3.3, does option -d in editconf really imply that the protein will be centered or is there still a bug (as in version 3.2.1) or am I missing something?ThanksIsabella___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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===End of original message text! === ___ 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] proper dihedrals
those are supposed to be in a parameters file. If not, look for some published paper about dynamics with a system that has those same atom sequences you listed. Maybe there's even a paper related you your actual research and it has the parameters you need.==Original message text===On Tue, 11 Jul 2006 13:14:32 EDT "ARGYRIOS KARATRANTOS" wrote:Hi all, according to the manual the proper dihedrals are set, using in the topologyfile(top file) the inner two atoms of the dihedral. But how i can set the twofollowing dihedrals, which have the same inner atomsC-O-C-HC-O-C-Cbut different external atoms, and of course different K values(KJ/mol)Argyris Karatrantos___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to gm! [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php===End of original message text=== ___ 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] dielectric constant
I think that is supposed to be changed in the parameters file. I really don't know. Ask David Spoel. I bet Penn State is looking nice today. ==Original message text=== On Fri, 07 Jul 2006 13:10:42 EDT "ARGYRIOS KARATRANTOS" wrote: could you please tell me how we can change the dielectric constant epsilon(r) in the topology file. this constant has the default value of 1. thanks in advance Argyris Karatrantos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 ===End of original message text=== ___ 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] dielectric constant
Hello, Gromacs administrators, I have a suggestion. In the online manuals can you explain how to read the output or log file after explaining how to use each command. For example, g_hbond Description Flags I/O How to read outputs * By the way, how do I read a .xvg from a G_hbond calculation? ==Original message text=== On Fri, 07 Jul 2006 13:10:42 EDT "ARGYRIOS KARATRANTOS" wrote: could you please tell me how we can change the dielectric constant epsilon(r) in the topology file. this constant has the default value of 1. thanks in advance Argyris Karatrantos ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 ===End of original message text=== ___ 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] Error
You are trying to convert a movie into a still picture. I don't think that's posible unless you freeze the frames. Check the Manual. bon chance ==Original message text=== On Fri, 07 Jul 2006 13:03:07 EDT "karamyog singh" wrote: Dear Users, When I try and convert my traj.xtc file to a .gro file I get the following error Reading frame 0 time0.000 Precision of traj.xtc is inf (nm) Using output precision of 0.001 (nm) Fatal error: DEATH HORROR prec () <= 0 in prec2ndec Can anyone tell me what is meant by it? Thanks, Karamyog Undergraduate student, IIT kharagpur. ===End of original message text=== ___ 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] What are the units for the results of the g_chi
Hi Gromac's users, I was checking the outputfile of g_chi and The numers did not seem right. What are the units of the dihedral angles? They can't be in degrees but Gromacs usually uses degrees for degrees some csome constants have radians. I don't know what are the units of this outputfile, can you tell me? -Diana ___ 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] H2O close to N-terms
Someone has written a script to calculate how may times H2O molecules get really close or bind to the N-terminals of a protein?(it's outer part, not the core) Or maybe someone nows how to calculate the N-terms interactions with the solvent? Anything related to this would help. ___ 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
