[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] make_ndx problem
Dear GMX users... i have a protein-peptide complex wherein peptide does not have one of the terminal carboxy oxygen atoms (i.e., it has -CO only). I designate A to peptide and B to protein chain. when i do pdb2gmx, it adds the missing O, so now the group is -COO. Now with this gro file, i tried to make some groups with make_ndx. when i select group 0 (system) or 1 (protein), and try to generate index file, i get the following error... *** glibc detected *** double free or corruption: 0x081b5bc0 *** Aborted but when i use any other groups to make some index file, i do not get any error Moreover, when i solvate the system, and use the resultant gro in make_ndx, i get no errors with any combination of groups!!! i am really confused please help... bharat ___ 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] make_hole
Dear freinds I want to make a hole in popc , i run below commands make_hole.pl -f .pdb -o .pdb -r 2.7 -lipat p8 -lipid pop grompp_hole -f .mdp -o .tpr -c .pdb -r .pdb -p .top but error is appear: one of the box vectors is shorter than twice the cut_off lenght. whould you please help me? best regard __ 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] QM method or basisset (CPMD) is not implemented
In God We TrustHello gmx usersWe compiled CPMD and Gromacs_qmmm and run ethane example , but it says :Fatal error:this QM method or basisset (CPMD) is not implementedWhat does it mean ? and what must we do?Thank you very much in advanceKarim MahnamInstitute of Biochemistry and Biophysics (IBB)Tehran University P.O.box 13145-1384Tehran Iran http://www.ibb.ut.ac.ir/ ___ 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] make_ndx problem
bharat v. adkar wrote: Dear GMX users... i have a protein-peptide complex wherein peptide does not have one of the terminal carboxy oxygen atoms (i.e., it has -CO only). I designate A to peptide and B to protein chain. when i do pdb2gmx, it adds the missing O, so now the group is -COO. Now with this gro file, i tried to make some groups with make_ndx. when i select group 0 (system) or 1 (protein), and try to generate index file, i get the following error... *** glibc detected *** double free or corruption: 0x081b5bc0 *** Aborted if this is reproducible then please file a bugzilla. but when i use any other groups to make some index file, i do not get any error Moreover, when i solvate the system, and use the resultant gro in make_ndx, i get no errors with any combination of groups!!! i am really confused please help... bharat ___ 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
