[gmx-users] ACPYPI announcement
Hi List! Well, it's a modest contribution and not properly released but I guess people may find it useful. So 'svn update' and check the website: http://code.google.com/p/acpypi/ often for any eventual update. It's ACPYPI, a tool based on Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. acpypi is pronounced as ace + pipe. Topologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER. NOTE: any topology and parameter files created by antechamber/acpypi (based on General Amber Force Field - GAFF) is intended to work with AMBER force fields only. Although I have seen people using ligand in GAFF and protein in CHARMM force field with apparently good results for docking, it would be interesting to investigate how a ligand in GAFF would work with a protein in OPLS/AA force field. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ 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] OPLS parameters for phospho-tyrosine
Dear All, Has anyone a topology for phosphorylated tyrosine residue in OPLS that can be shared? Sincerely, -Maria -- -- Maria G. Technical University of Denmark Copenhagen ___ 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] deprotonated cys
But of course then you also need to parameterize it, which is not a trivial task. OPLS does not have parameters for a cys thiolate; I'm not sure about other ff's. If you go back to the opls paper, you can follow the route by which they parameterized other ionized sc's. I have been considering doing this myself, but it seems complicated for my slight experience level with qm. Remove the hydrogen from the rtp file and re-work the charge based on a guess at your own peril. I suppose that there are things that you could do with such a model, but if the cys is deeply relevant then you should really find consistent parameters or develop them yourself. Chris. -- original message -- i want to ask you question about how can i deprotonate or use deprotonated cysteine because I have protein with “cys” in active site, and I want to use deprotonated “cys”. when i run “pdb2gmx “ no option appearing of choosing Cys deprotonated state possibility That's correct. You can edit the rtp file to add support for CYS-, e.g. name it CYM and then name the residue in your pdb file CYS instead of CYS as well. ___ 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] settle issue
Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and seem to find a hint: in gromacs simulation the intra-molecular atom-atom distance (should be fixed by settle) fluctuation is quite large! How can one increase the accuracy of settles in gromacs? Settle is analytical and there is no tolerance. However you may be using settle with the SPC parameters (unlikely though). Maybe you should turn on the Dispersion Correction to the pressure (EnerPres). That gives a similar density difference. Regards Yuguang ___ 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 -- 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 ___ 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] AFM: .pdo output format
Dear All, I am using pull code to perform AFM on some protein. My pull dimensions are pulldim as Y Y Y for x,y and z coordinates. the output .pdo files are generated, and as far as I have understood, it will get the .pdo output as: time (t), position of ref group (xr,yr,zr), position of pulled group(xp,yp,zp) and position of spring (xs,ys,zs) and accordingly, I am getting 10 columns output: t xr yr zr xp yp zp xs ys zs In the manual it is written that position of pulled group and spring are in absolute coordinates. Subtract the reference coordinate to get the position relative to the pulled group. which I suppose means that the extension (difference between the pulled group and reference group) should be like = dist=sqrt( (xr-xp)2 + (yr-yp)2 + (zr-zp)2 ) But when I am calculating this way, I am getting very less distance values, which otherwise, when i am doing geometry calculations, they are coming quite higher. I am quite confused. I think I am missing something very important which I am not able to make out. If anyone can please help me out Thanks a lot in advance, Regards, Monika Sharma ___ 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] What's the default pbc of Gromacs trajectories?
Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was whole, which means no broken molecules. But I just found it's not the case for the latest version, since I can see broken lipids for my membrane system using ngmx. I'm just wondering what's the default pbc for the latest Gromacs version and whether there is a way to change it before MD simulations. Thanks for your help. Lanyuan Lu _ MSN 中文网，最新时尚生活资讯，白领聚集门户。 http://cn.msn.com ___ 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] What's the default pbc of Gromacs trajectories?
LuLanyuan wrote: Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was whole, which means no broken molecules. But I just found it's not the case for the latest version, since I can see broken lipids for my membrane system using ngmx. I'm just wondering what's the default pbc for the latest Gromacs version and whether there is a way to change it before MD simulations. I think you are asking two separate questions. From trjconv -h you can find the default behavior for PBC treatment, which is none, as in, leave the coordinates alone. The PBC behavior of an MD simulation is specified in the .mdp file. Removal of PBC from broken starting structures should be the first step in the simulation. -Justin Thanks for your help. Lanyuan Lu _ MSN 中文网，最新时尚生活资讯，白领聚集门户。 http://cn.msn.com ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] g_rmsf
sudheer babu wrote: Hi, I would like to calculate B-factor of protein, so I performed command like this g_rmsf -f .xtc -s .tpr -res -o fluctuate.xvg -od devi.xvg it has run without error.Now i am bit doubting that which .xvg file have to take for plot B-factor values? I think you have not specified the correct options. Check g_rmsf -h and read about the -oq option. -Justin B-factor is nothing but thermal devation of atoms. I think, I should take dev.xvg for plotting B-factor values, if it is coorect, then what' s the need for producing fluctuate.xvg? may be this is trivial question. Could anyone help me pls. Thanks alot in advance ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] What's the default pbc of Gromacs trajectories?
Thanks for your reply. I just checked the online manual for .mdp. But I didn't find an option to change output pbc types. If I need the output trr file to be whole as that from an older version, can I set it up anywhere? I understand I can use trjconv to convert trr files. But usually trr files are huge and the convertion takes time. Thanks, Lanyuan Lu Date: Mon, 28 Jul 2008 17:07:30 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] What's the default pbc of Gromacs trajectories? LuLanyuan wrote: Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was whole, which means no broken molecules. But I just found it's not the case for the latest version, since I can see broken lipids for my membrane system using ngmx. I'm just wondering what's the default pbc for the latest Gromacs version and whether there is a way to change it before MD simulations. I think you are asking two separate questions. From trjconv -h you can find the default behavior for PBC treatment, which is none, as in, leave the coordinates alone. The PBC behavior of an MD simulation is specified in the .mdp file. Removal of PBC from broken starting structures should be the first step in the simulation. -Justin Thanks for your help. Lanyuan Lu _ MSN 中文网，最新时尚生活资讯，白领聚集门户。 http://cn.msn.com ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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 _ Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！ http://get.live.cn/product/photo.html___ 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] What's the default pbc of Gromacs trajectories?
LuLanyuan wrote: Thanks for your reply. I just checked the online manual for .mdp. But I didn't find an option to change output pbc types. If I need the output trr file to be whole as that from an older version, can I set it up anywhere? What you are probably seeing is a visualization artifact, but you haven't described things very thoroughly. In fact, mdrun does not write broken molecules; everything should be whole. Like I said before, as soon as you start a simulation, all broken molecules are made whole. Such behavior is defined in the topology. If there is a bond between two atoms at a given distance, mdrun knows these atoms are bonded, even if they initially appear across the box from each other. I understand I can use trjconv to convert trr files. But usually trr files are huge and the convertion takes time. So write your output in .xtc format. Use the nstxtcout option in the .mdp file. -Justin Thanks, Lanyuan Lu Date: Mon, 28 Jul 2008 17:07:30 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] What's the default pbc of Gromacs trajectories? LuLanyuan wrote: Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was whole, which means no broken molecules. But I! ! just found it's not the case for the latest version, since I can see broken lipids for my membrane system using ngmx. I'm just wondering what's the default pbc for the latest Gromacs version and whether there is a way to change it before MD simulations. I think you are asking two separate questions. From trjconv -h you can find the default behavior for PBC treatment, which is none, as in, leave the coordinates alone. The PBC behavior of an MD simulation is specified in the .mdp file. Removal of PBC from broken starting structures should be the first step in the simulation. -Justin Thanks for your help. Lanyuan Lu _ MSN 中文网，最新时尚生活资讯，白领聚集门户。 http://cn.msn.com ! ! ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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 用 Windows Live Spaces 展示个性自我，与好友分享生活！ 了解更多信息！ http://spaces.live.com/?page=HP -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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
