Re: [gmx-users] ligand topology
Quoting Blaise Mathias-Costa [EMAIL PROTECTED]: hello all,How to get the topology for a ligand, for which there is no information available with the gromacs default libraries!! Thanks in advanceBlaise Try PRODRG: http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ -Justin == Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://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] Chitosan topology
Hi Antonello, Note that parameterization of compounds is not for the faint of heart (http://wiki.gromacs.org/index.php/Parameterization). For chitosan, you first want to get the parameters for one building block right. In case you want to use the GROMOS force field, search papers of Roberto Lins, who parameterized the sugars for the GROMOS 45a3 force field. Then go for di- and tri-glycans and be sure that these give reasonable behaviour. If that works, you can go for the larger ones, ideally writing a .rtp building block CTS and contributing it on the gromacs contributions site :) Note also that I'm conveniently neglecting any work you presumably did w.r.t. parameterization, assuming that you didn't do it in a correct manner, since you mention you get (otherwise unspecified) poor results. If you think I'm too harsh on you, you should really consider taking Yang Ye's advice and give more information about the things you did and the nature of your poor results. Cheers, Tsjerk On 7/31/07, Yang Ye [EMAIL PROTECTED] wrote: Hi, Please describe clearly your poor results. Regards, Yang Ye On 7/31/2007 10:55 PM, Antonello wrote: Dear gromacs users, i apply to your kind attention to know if someone have already parametrized the chitosan structure. I am trying to do it but with poor results. Can you help me? Thanking in advance Dipartimento di Medicina Sperimentale Universita' degli Studi di Parma ___ 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 -- 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 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] Chitosan topology
Dear gromacs users, i apply to your kind attention to know if someone have already parametrized the chitosan structure. I am trying to do it but with poor results. Can you help me? Thanking in advance Dipartimento di Medicina Sperimentale Universita' degli Studi di Parma ___ 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] Chitosan topology
Hi, Please describe clearly your poor results. Regards, Yang Ye On 7/31/2007 10:55 PM, Antonello wrote: Dear gromacs users, i apply to your kind attention to know if someone have already parametrized the chitosan structure. I am trying to do it but with poor results. Can you help me? Thanking in advance Dipartimento di Medicina Sperimentale Universita' degli Studi di Parma ___ 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] Creating topology file for TBA cation using OPLS force field
Hi all! I'm just a beginner user of Gromacs, that's why my question may seem strange to you. But I hope, that somebody can help me in solving my problem. The point is that I'm trying to perform the analysis of tetrabutylammonium cation solvatation using OPLS force field. Earlier i've modelled tetrametylammonium cation with same force field; the topology *.itp file for TMA was created, using The Dundee PRODRG Server: itp-file was created for some Gromacs force field, and than modified by definition of the UA-groups according to OPLS UA-types. This way is unsuitable for determination of TBA topology, 'couse in this case all-atom determination should be performed. So that's why I'm asking your advise what should I do. Thanks a lot! ___ 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] Building Topology of a Drug (using the ff of your choice)
Hi Mitch, thanks. I'd like to use the OPLSA ff, to compare with other simulations that I've run. So I can use the PRODRG to build an initial, then look at the OPLSA ff to modify it, as you've suggested. I was just wondering if there was a quick and easy way to do it, but I guess not! Thanks, Arneh Mitchell J Stanton-Cook wrote: Hi, You could use PRODRG to build an initial topology and then use the FF definition in you gromacs distribution to edit to suit. On the PRODRG website, there is a link to the top right had of the page if memory serves me correctly to a beta server that will generate topology files consistent with the 43a1 FF. Cheers Mitch On Thu, 2007-02-15 at 17:48 -0800, Arneh Babakhani wrote: Hi , I'd like to build a topology of a Drug. I'm aware of the PRODRG website. But if my understanding is correct, on this website, you can only build using one forcefield (GROMOS87). How does one build a topology using a different force field (say for instance, oplsaa)? Is there a simple way to do it, Thanks, Arneh ___ 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 ___ 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:Building Topology of a Drug (using the ff of your choice)
Arneh, How does one build a topology using a different force field (say for instance, oplsaa)? Is there a simple way to do it, I think OpenEye (or someone else, I forget whom) has some sort of automatic parameterization tool for OPLS that automatically generates parameters. Of course, this is not the same as a topology. Another option is using the Antechamber package. If you have AMBER, I have a conversion script you can use that will convert Antechamber's AMBER topologies and coordinates into GROMACS topologies and coordinates. This is pretty much a fully automatic process, so it is fairly painless. David Hi, David, That is very good. Could you send it to me or put it online so that every one can download it? Zhongqiao ___ 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] Re:Building Topology of a Drug (using the ff of your choice)
On 2/17/2007 12:01 PM, Hu Zhongqiao wrote: Arneh, How does one build a topology using a different force field (say for instance, oplsaa)? Is there a simple way to do it, I think OpenEye (or someone else, I forget whom) has some sort of automatic parameterization tool for OPLS that automatically generates parameters. Of course, this is not the same as a topology. Another option is using the Antechamber package. If you have AMBER, I have a conversion script you can use that will convert Antechamber's AMBER topologies and coordinates into GROMACS topologies and coordinates. This is pretty much a fully automatic process, so it is fairly painless. David Hi, David, That is very good. Could you send it to me or put it online so that every one can download it? Zhongqiao Antechamber has its own website. Please use Google and there is a accompanying tutorial, too. ___ 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] creating topology files
Mark Abraham wrote: --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1180 Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. --- This is being caused by the R-B dihedrals. (This error message should be improved, gromacs team.) [...] Any suggestions? This is the generic topology file parsing stuff where one doesn't necessarily known which type of function is being read, only what parameters to expect... -- Groetjes, Anton _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ | | | If You See Me Getting High, Knock Me Down (RHCP)| |_|___| ___ 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] creating topology files
Title: creating topology files Fellow gmx users, I am trying to create a topology file for TFE using the olpsaa/l force field to simulate a peptide in a mixed solvent. I created a molecule.itp file (as it was suggested in the manual), a molecule.gro file for TFE and I was able to place the several TFE and water molecules in a box. When I ran grompp before equilibrating the system, the program was expecting a topology file, so I created one instead of the .itp file. After trying grompp once again, I received an error message that read: --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1180 Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. --- My topology file is attached to this message. I left the second dihedral parameters blank since there are no planar entities in TFE, and the [ pairs ] have a value of zero since the opls forcefield calculates 1-4 interactions by scaling. Could you suggest any changes to my topology file? Thank you in advance, Michael Owen tfe_mike.top Description: tfe_mike.top ___ 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] creating topology files
Owen, Michael wrote: Fellow gmx users, I am trying to create a topology file for TFE using the olpsaa/l force field to simulate a peptide in a mixed solvent. I created a molecule.itp file (as it was suggested in the manual), a molecule.gro file for TFE and I was able to place the several TFE and water molecules in a box. When I ran grompp before equilibrating the system, the program was expecting a topology file, so I created one instead of the .itp file. After trying grompp once again, I received an error message that read: The idea is that the .itp file can be #included in multiple .top files. --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1180 Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. --- This is being caused by the R-B dihedrals. (This error message should be improved, gromacs team.) Your [ dihedrals ] have only four parameters, and they need 6 (or 12 for a free-energy perturbation calculation), so go back and find what you did wrongly. My topology file is attached to this message. I left the second dihedral parameters blank since there are no planar entities in TFE, and the [ pairs ] have a value of zero since the opls forcefield calculates 1-4 interactions by scaling. That sounds like asking for grompp to incorporate functions that evaluate to zero, rather than the pertinent defaults. I'd read the manual carefully, and probably eliminate these [ pairs ]. 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
[gmx-users] norleucine topology
dear list, to get a topology for norleucine i combined parameters from LEU (N,CA,CB, plus H´s, C, O) and MET (CG, CE, plus H´s). to get CD and its H´s i took parameters from MET CG as well. finally i adjusted the charges of CG and CD to get a residue topology with zero charge. can it be that easy??? merc -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer ___ 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] norleucine topology
merc mertens wrote: dear list, to get a topology for norleucine i combined parameters from LEU (N,CA,CB, plus H´s, C, O) and MET (CG, CE, plus H´s). to get CD and its H´s i took parameters from MET CG as well. finally i adjusted the charges of CG and CD to get a residue topology with zero charge. can it be that easy??? merc in this case, yes. which ff did you use? can you contribute the rtp and hdb entries? -- 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 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] steroid topology
Hello everyone, I have been having trouble with a topology I created for androst-5-ene-3,17-dione (GROMOS 96 force field). I have found the molecule to bend inwards withing 100 ps of equilibration, something which has not been seen by others who have used CHARMM or AMBER. I have also tried to convert the topology generated by the PRODRG DUNDEE server for GROMACS but had the same issues with it. Can anyone throw any pointers my way, or better still a steroid topology which works Regards Dhruv __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] steroid topology
Hello, I have been having trouble with a topology I created for androst-5-ene-3,17-dione (GROMOS 96 force field). I have found the molecule to bend inwards withing 100 ps of equilibration, something which has not been seen by others who have used CHARMM or AMBER. I have also tried to convert the topology generated by the PRODRG DUNDEE server for GROMACS but had the same issues with it. Can anyone throw any pointers my way, or better still a steroid topology which works Regards Dhruv __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] Need topology for selenomethionine
Hi all, Has anybody built a gromax topology for selenomethionine? How the topology can be incorporated into the existing gromacs topology files? thanks in advance. sridhar -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ 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] Need topology for selenomethionine
Sridhar Acharya wrote: Hi all, Has anybody built a gromax topology for selenomethionine? How the topology can be incorporated into the existing gromacs topology files? It might exist on the website. You just need to replace the sulphur by Se, probably with a slightly larger sigma. Check literature as well for the force field you want. thanks in advance. sridhar ___ 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 -- 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 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] No topology
Title: No topology I just want to generate the topology of one protein with water. Previously I had obtained the archive .gro from a .pdb, I used editconf to make a box after I used genbox to add waters to protein. The archive .gro is generated but I have tried many times and with other proteins and I can't generate the archive .top I am using the correct command: genbox -cp protein.gro -cs spc216.gro -o proteinw.gro -p proteinw.top The error that I recive is: Processing topology --- Program genbox, VERSION 3.3.1 Source code file: futil.c, line: 340 File input/output error: proteinw.top --- I will thank if someone can help me. -- Edgar Mixcoha Hernndez, Chemist, BSc Laboratorio de Bioqumica, Edificio de Posgrado Escuela Nacional de Medicina y Homeopata, IPN Lab +52 55 5729 6000 ext 55562 Mobile +52 55 2955 2219 __ ___ 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 topology
Edgar Mixcoha Hernández wrote: I just want to generate the topology of one protein with water. Previously I had obtained the archive .gro from a .pdb, I used editconf to make a box after I used genbox to add waters to protein. The archive .gro is generated but I have tried many times and with other proteins and I can't generate the archive .top I am using the correct command: genbox -cp protein.gro -cs spc216.gro -o proteinw.gro -p proteinw.top pdb2gmx The error that I recive is: *Processing topology --- Program genbox, VERSION 3.3.1 Source code file: futil.c, line: 340 File input/output error: proteinw.top --- * I will thank if someone can help me. -- Edgar Mixcoha Hernández, Chemist, BSc Laboratorio de Bioquímica, Edificio de Posgrado Escuela Nacional de Medicina y Homeopatía, IPN Lab +52 55 5729 6000 ext 55562 Mobile +52 55 2955 2219 __ ___ 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 -- 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 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: topology transformation
Anthony Cruz wrote: Thank you for your answer. I find it to day searching the mailing list because I have some problems with the mail and I dont receive this mail. I try the beta version but I got confised because i dont see the GROMOS terminology ej. gb_x, ga_x ect. If I use the beta version i could use the file as I get it from PRODRG? or I need to change it??? I always created .rtp building blocks for my residues and converted the explicit PRODRG values to GROMOS nomenclature with the help of ffG43a1bon.itp. But it is also possible to use explicit values with 43A1, one of my students did it like this (PRODRG has some more angle types than standard 43A1). You may check with gmxdump if the resulting .tpr is OK. Regards Christian ___ 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
