Re: [gmx-users] Selection of multiple residues
Hi, I assume you want to select a range of residues, not some scattered amino acids.. So just check from your gro-file the atom numbers of begin and end of the region you need and use the information to select and copy the indices from an existing index-file to create a new group. Best regards, Björn Hello, I want to select 300 residues out of my 1000 residue protein and make an index out of it. make_ndx does not seem to have a simple method to do this. These are all residues in the same chain. How does one do this ? Sincerely -Maria -- Maria G. Technical University of Denmark Copenhagen -- Dr. Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: [EMAIL PROTECTED] Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml ___ 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] Selection of multiple residues
Hi, index files contain groups of atoms represented by their atom number. Just check an index file how it is constructed. By default, there are several groups (System, Protein, Protein-H, etc.). So if you want to work with a range of residues (e.g. 1-300) just create a new group and copy the atom indices of those residues (1-) from another group into it (But carefully check from which existing group you are copying, depends on what you are interested). Best regards, Björn to select and copy the indices from an existing index-file to create a new group I am sorry I did not understand the meaning of the above ? I will have the first atom number and the last atom number, and then ? How do I copy the indices ... On Fri, Feb 22, 2008 at 10:58 AM, Bjoern Windshuegel [EMAIL PROTECTED]mailto:[EMAIL PROTECTED] wrote: Hi, I assume you want to select a range of residues, not some scattered amino acids.. So just check from your gro-file the atom numbers of begin and end of the region you need and use the information to select and copy the indices from an existing index-file to create a new group. Best regards, Björn Hello, I want to select 300 residues out of my 1000 residue protein and make an index out of it. make_ndx does not seem to have a simple method to do this. These are all residues in the same chain. How does one do this ? Sincerely -Maria -- Maria G. Technical University of Denmark Copenhagen -- Dr. Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: [EMAIL PROTECTED]mailto:[EMAIL PROTECTED] Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtmlhttp://www.uku.fi/farmasia/f ake/modelling/index.shtml ___ gmx-users mailing list gmx-users@gromacs.orgmailto: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]mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Maria G. Technical University of Denmark Copenhagen -- Dr. Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: [EMAIL PROTECTED] Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml ___ 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] calculating B-factor
Hi, check out g_rmsf (options -oq, -q, -ox), rmsf can be converted into B-factors. Best regards, Björn Dear users Is it posible to calculate B-factor for a protein using gromacs? Pragya Detailed profiles 4 marriage! Only at Shaadi.com Try it!http://ss1.richmedia.in/recurl.asp?pid=107 -- Dr. Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: [EMAIL PROTECTED] Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml ___ 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] Trajectory files are too big
Hi, you can easily restrict the amount of data if you set the frequency of writing out coordinates accordingly. Check the manual page 138 (7.3.7, output control). The standard settings (100) are quite small, I recommend to use at least 1000 for writing out coordinates. So the amount of data should be reduced significantly. Best regards, Björn Dear Gromacs Users, After a long time I am working with gromacs. Though at the starting I got some problem in installation with the rpm, (a conflict error with mono-web) I installed it anyway forcefully. Problem is the trajectory files that I am getting are too big. I have run a mdrun for 2ns on a protein+water system consisting of 60149 atoms in 18875 residues (as after running 'genbox' using spc216.gro). The .xtc, and .trr files I am getting are of 19GB and 12GB respectively. Is this normal, or I have some problem with my gromacs? My hard disk space is 80GB. I am just worrying about what should I do if I will have to run it for 4ns or more than that?? If these files are so big how many MD will I be able to run? Is double precision installation of gromacs helpful? will I get these trajectory files in some compressed format?? Please help. Nabajyoti Goswami Ph.D Student. Center for Biotechnology, Anna University, Chennai-600025 Tamil Nadu. Mobile: 09840487093 -- Dr. Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: [EMAIL PROTECTED] Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml ___ 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] merger ligand and protein to constriant
Hi, you can also have different chains (Protein and Ligand) and constrain them. Using the -merge option you can merge the ligand into the protein but for that you need the topology for the ligand (as rtf, not from prodrg). If you use Prodrg-topology you first set up the protein without ligand. Then you include the topology for the ligand into the protein topology (#include XXX.top) and also the coordinates in the protein-gro-file. Then you can proceed with adding water, ions, etc. Then you can also apply position-restraints. By the way, as far as I know Sonja Schlimme has used a similar kind of setup in her MD simulations. So you could also ask her. Best regards, Björn Hi all I already look in the turorial however that is not the thing that I try to look for. I would like to merge the ligand into the protein and then make the contrain between two atoms, one from the liagand and one from the protein. However, as far as I know, I can do the constraint or restraint just in the one chain. I cant do that with the different chain. So that i try to merge ligand chain and protein chain. I tried to do that with pdb2gmx but it is not work. So that i would like to know is there any way to merge the ligand chain with the protein chain. Thanks for all your suggstions Best Regard Kanin -- Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 ___ 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] trjconv problem
Hi, thanks for the tips. First I used the information of the exact time I got from g_cluster which did not work (t=5590.093). So I used trjconv to convert the whole trajectory in a pdb-file from which I got the exact time (t=5590.00049) of the frame to be extracted that was different compared to that in g_cluster. By using that as input for trjconv I finally could extract the frame. The -dump option did not work without specifying the exact frame time. Best regards, Björn It might be a rouding problem, so if you want to extract the single frame at time 5590, you might want to try trjconv -b 5589.9 -e 5590.1 -o frame.pdb ... If it still doesn't work: In gromacs 3.3 there was a bug that caused trjconv not to find frames. As far as I know the bug was fixed in Version 3.3.1. cheers, jochen hi, similar happened to me, when i used the -b and -e flags of trjconv. to me it seemed that if you do not hit exactly the time frame as written in the trr file, trjconv will not output anything. when i used the -dump flag it worked, because then frames near the specified time are dumped. hope that helps. marc -- Bjoern Windshuegel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 ___ 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] trjconv problem
Hi everybody, I am trying to extract some frames from my md simulation using trjconv. For some frames this works fine but for others of the same simulation I get the following error message (for frame after 5590 picoseconds): Skipping frame500 time 5250.000 Setting output precision to 0.001 (nm) WARNING no output, trajectory ended at 5590 The trajectory has a length of 10 ns. I could successfully extract frames for 4310 and 8950 but not 3110, 5590 and 7020 picoseconds. Any idea what could be the problem? Best regards, Björn -- Bjoern Windshuegel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 ___ 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
