Re: [gmx-users] Help with nitrile group in complx protein-ligand md
Jocley Araujo wrote: Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the error part. But lots of numbers appear before this error. Program mdrun, VERSION 4.0.4 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1522) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- These ligands all have in common the nitrile group linked to an aromatic ring. I am using the gromos 53a6 forcefield. The minimization step ran normally for these complexes, so I only had problems when I tried to run the md simulations. I have alreay tryed some of the solutions given by the gmx user`s list like subtituting LINCS for SHAKE. Maybe my error has something to do with the nitrile group. Has anyone had any problem like this before? Something is physically unrealistic about your system, leading to LINCS crashing. Where did you get your parameters for the nitrile group? If this is the common thread for the systems that crash, you can bet that whatever parameters you are using are not reliable. -Justin I would like some help on the matter Jocley ___ 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 -- 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://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
Re: [gmx-users] Help with nitrile group in complx protein-ligand md
Jocley Araujo wrote: Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the error part. But lots of numbers appear before this error. Program mdrun, VERSION 4.0.4 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1522) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- These ligands all have in common the nitrile group linked to an aromatic ring. I am using the gromos 53a6 forcefield. The minimization step ran normally for these complexes, so I only had problems when I tried to run the md simulations. I have alreay tryed some of the solutions given by the gmx user`s list like subtituting LINCS for SHAKE. Maybe my error has something to do with the nitrile group. Has anyone had any problem like this before? I would like some help on the matter You need to define a virtual site. If you have C1-C2#N3 you want to make a bond (constraint) between 1 and 3, and define 2 as a vsite (check manual). Jocley ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Help with nitrile group in complx protein-ligand md
Hello I had a problem with mdrun while trying to run trajectories for protein ligand complexes. I`ve already done successful calculations with 60 complexes, unfortunately 4 complexes gave the following error. The entire output is too big to copy, so I have only copied the error part. But lots of numbers appear before this error. Program mdrun, VERSION 4.0.4 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1522) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- These ligands all have in common the nitrile group linked to an aromatic ring. I am using the gromos 53a6 forcefield. The minimization step ran normally for these complexes, so I only had problems when I tried to run the md simulations. I have alreay tryed some of the solutions given by the gmx user`s list like subtituting LINCS for SHAKE. Maybe my error has something to do with the nitrile group. Has anyone had any problem like this before? I would like some help on the matter Jocley ___ 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
