Well... There is one line in try2-water.pdb, shows as below
TITLE Protein REMARK THIS IS A SIMULATION BOX CRYST1 86.185 86.185 86.185 60.00 60.00 90.00 P 1 1 Do you think something was wrong during genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+ -nname CL- Thanks, lina ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] Sent: Tuesday, June 15, 2010 1:41 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] the box lengths Well, there's ya problem :-) That specifies the box dimensions. Have a look at try2-water.pdb as well, then you should be able to pin down where the issue has arisen. Appears that one of those steps have failed to write the box dimensions. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of #ZHAO LINA# > Sent: Tuesday, 15 June 2010 3:37 PM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] the box lengths > > There is none CRYST1 line in the file try2-water-ions.pdb. > > Thanks and regards, > > lina > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au] > Sent: Tuesday, June 15, 2010 1:24 PM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] the box lengths > > What is the contents of the CRYST1 line in the file try2-water- > ions.pdb? > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > --------------------------------- > When the only tool you own is a hammer, every problem begins to > resemble > a nail. > -- > 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 > -- > 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 -- 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 -- 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