dear justin I transfer gro files from linux to windows through SSH secure shell program. I added 10 Na ions by genion command but in gro file following case is appeared:
7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991 7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803 7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903 7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485 7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725 7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660 7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264 7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767 7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022 7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437 *7218Cl Cl23137 0.000 0.000 0.000 0.0000 0.0000 0.0000 * 6.15463 6.21503 6.20117 I deleted line of 7218Cl Cl23137 0.000 0.000 0.000 0.0000 0.0000 0.0000 in top file following case is appeared: [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 SOL 7117 Na 10 Cl 0 I deleted last line. I am using amber03 force field in gromacs program to study interaction of pr-dna.
-- 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
