Re: [gmx-users] problem while running grompp command
rashi parihar wrote: Hi all. I am doing dynamics studies of protein-ligand dynamics.When I am running grompp command error is coming atomtype SDMSO NOT FOUND . I checked in drg.itp file [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OM 1 LIG OXT 1 -0.758 15.9994 2 C 1 LIG C 1 0.362 12.0110 3 OM 1 LIG O 1 -0.758 15.9994 4 CH1 1 LIG CA 1 0.154 13.0190 5 NL 1 LIG N 2 0.590 14.0067 6 H 1 LIG H3 2 0.001 1.0080 7 H 1 LIG H4 2 0.002 1.0080 8 H 1 LIG H1 2 0.002 1.0080 9 CH2 1 LIG CB 2 0.109 14.0270 10 CH2 1 LIG CG 2 0.109 14.0270 11 SDMSO 1 LIG SD 2 0.974 32.0600 now in 11th row SDMSO IS PRESENT.How can I solve this problem?plz help me!!! The problem is that your topology file is calling SDMSO, which does not exist. All Gromos force fields use SDmso - capitalization matters. Check the .atp file for your chosen force field to be sure of the requirements of the force field. It looks to me like this is a PRODRG output. Please see the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips as to why you should likely not use this topology in its current state for anything. -Justin -- images[12] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem in running grompp
hi, i am simulating a membrane protein inside dppc bilayer and in this regard i am following justin's tutorial. but i ma facing a problem in running grompp...whenever i run it is giving error Program grompp, VERSION 4.0.5 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (1A68_genbox.gro, 49128) does not match topology (1A68.top, 48628) now how to solve this problem? i have first generated the lipid box with the protein then solvated it. i really need little bit of help to proceed to the next step... Thaking You... Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in running grompp
--- On Mon, 8/6/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] problem in running grompp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 8 June, 2009, 4:47 PM Samik Bhattacharya wrote: hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows ''Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 843 Fatal error: Atomtype CA not found'' but is not CA the main chain alpha carbon...why is not grompp taking CA then? i can't make out where the problem lies? i little help on this shall be very encouraging. If you're seeing this error, then you've done something wrong when combining lipid.itp with the Gromos force field file. -Justin Thank You Shamik Thank you Justin for the answar. but now how to solve it? where should i make changes to correct that? pls let me know what to do... waiting for your answar Thank you again.. ___ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in running grompp
Samik Bhattacharya wrote: Thank you Justin for the answar. but now how to solve it? where should i make changes to correct that? pls let me know what to do... waiting for your answar Thank you again.. CA is not an alpha-carbon, it is a ffgmx atom type. So, therefore, you have copies some ffgmx parameters into the ffG53a6nb_lipid.itp that the tutorial describes, probably from the ;; parameters for lipid-GROMOS interactions which the tutorial clearly tells you to delete. -Justin ___ gmx-users mailing listgmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 /mc/compose?to=gmx-us...@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in running grompp
hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows ''Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 843 Fatal error: Atomtype CA not found'' but is not CA the main chain alpha carbon...why is not grompp taking CA then? i can't make out where the problem lies? i little help on this shall be very encouraging. Thank You Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in running grompp
Samik Bhattacharya wrote: hi i am simulating a membrane protein in POPC bilayer and for that i am following justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing some problems in running the grompp command. after the solvation when i am going to run grompp, it is generting an error as follows ''Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 843 Fatal error: Atomtype CA not found'' but is not CA the main chain alpha carbon...why is not grompp taking CA then? i can't make out where the problem lies? i little help on this shall be very encouraging. If you're seeing this error, then you've done something wrong when combining lipid.itp with the Gromos force field file. -Justin Thank You Shamik Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! http://in.rd.yahoo.com/tagline_Travel_1/*http://in.travel.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in running grompp
Hello, when I run grompp I get the following error message always. Whoever has a correct fix to get rid of this error message and get the actual result, Please suggest. Thanking you Dr. Victor A. Doss _ The new Windows Live Messenger. You don’t want to miss this. http://www.microsoft.com/india/windows/windowslive/messenger.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
