Hi Mohsen, I think rotating a molecule with editconf will not rotate the box. Then again, if it did, it would result in a box violating Gromacs requirements. Either way, it's not going to work like that. Build a new box after rotation... And have a good look at what you're actually trying now by taking the rotated system and stack it a few times using genconf -nbox 2 2 2
Cheers, Tsjerk On Jan 6, 2011 7:22 PM, "mohsen ramezanpour" <[email protected]> wrote: Dear Amit I entered these commands for rotating box: editconf -f conf.gro -o output.pdb -rotate 0 0 25.4 and then: editconf -f output.pdb -o newbox.pdb -rotate 0 127.67548 0 as a result my molecul is located out of box totally,of course drug and protein are bind to eachother yet. thanks in advance for your attention and reply On Tue, Jan 4, 2011 at 1:25 PM, Amit Choubey <[email protected]> wrote: > > Could you post the e... -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
