[gmx-users] How to view and analysis the result trajectory of g_covar?
Hi dear friends, I just get trajectory files using "g_covar". But how can I view this .trr file? I tried VMD and gOpenmol, etc and do not work. Thanks. SJ Huang -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. ___ 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] Ligand often slips out from the binding site in MD; is it natural?
I am doing MD of a ligand-protein complex derivated from docking, but I found that often the ligand slipped out slowly from the binding pocket. I then performed some MD simulations of several complex ligand-receptor complex obtained from PDB database, but no similar phenomena was watched. Is it natural for a ligand to slip from pocket frequently? Or does it indicate that my complex model derivated from docking is unreasonable? What should I do? Thanks to all. Shanjie Huang -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - And now for something completely differentÂ… ___ 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] Re: How to generate average C-alpha fluctuation during MD of every AA residue?
Thanks my friend, I have solve this problem with your kindly help. > Message: 4 > Date: Thu, 23 Mar 2006 08:56:27 +0100 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] How to generate average C-alpha fluctuation > during MD of every AA residue? > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Shanjie Huang wrote: > > Hi my dear friends, > > > > I just learn to use gromacs this days and I found a lot of figures in > > research articles that illustrates the average C-alpha fluctuation > > during MD of every AA residue, which can show very clearly that which > > part of protein is stable and which is flexible. But I examined the > > tutor and online manual for every commands yet cannot find the method. > > Please give me a hand. Thanks a lot. > > > > Shanjie Huang > g_rmsf > > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - Same, same, but differentÂ… ___ 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] How to generate average C-alpha fluctuation during MD of every AA residue?
Hi my dear friends, I just learn to use gromacs this days and I found a lot of figures in research articles that illustrates the average C-alpha fluctuation during MD of every AA residue, which can show very clearly that which part of protein is stable and which is flexible. But I examined the tutor and online manual for every commands yet cannot find the method. Please give me a hand. Thanks a lot. Shanjie Huang -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ 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] Why my protein always falls out of the water box?
Hi dear friends, I performed a molecular dynamics of a ligand-receptor complex for 5ns; but I found that my complex always fall out from the water box quickly in the first 1ns. What may be the problem? Can I constrain some residues which are far away from the active site to aviod this problem? But I am worry about the extra constrain would interfere my MD result, for in the normal situation there should be no constrains. Thanks. -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ 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] genbox fatal error with ligand-receptor complex: realloc for atoms_solvt->atomname : No such file or directory
Hi, I am working on a molecular dynamics of a receptor-ligand complex. I created the .gro files for receptor and ligand separatedly and merged them together, making sure the atom numbers are continuous. In the .top file of receptor I have put " #include "ligand.itp" " and append a line for ligand in [molecule section]. Then I executed "editconf" successfully. When I execute: genbox -cp receptor.gro -cs spc216.gro -o receptor_1.gro -p receptor.top Error occured: --- Reading solute configuration CERM PROTESE Containing 982 atoms in 100 residues Initialising van der waals distances... Opening library file /gdata/gromacs/share/top/vdwradii.dat Opening library file /gdata/gromacs/share/top/aminoacids.dat Reading solvent configuration "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 516x487x422 boxes Fatal error: realloc for atoms_solvt->atomname (-8686336 bytes, file genbox.c, line 390, atoms_solvt->atomname=0x0x101bbs98): No such file or directory What should I do then? Please give me a hand. Thanks. Sincerely MC Yan -- Shanjie Huang [EMAIL PROTECTED] -- http://www.fastmail.fm - The professional email service ___ 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
