Thank you so much.
On 9/11/07, Yang Ye <[EMAIL PROTECTED]> wrote: > > On 9/12/2007 12:39 AM, Wang Qin wrote: > > Hi Yang, > > I was thinking to set mass_B to 0 but what I was supposed to do > > is converting dummy atoms to H atoms. In my opinion, it wouldn't be H > > atoms if I set the mass to 0. Am I thinking wrong? > it's an H as long as it shares the same VDW as H and it carries the same > charge as H. > > Thank you. > > > > Regards, > > Qin > > > > On 9/11/07, *Yang Ye* <[EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>> wrote: > > > > you have set the mass_B to 0 as well. > > > > On 9/11/2007 10:54 PM, Wang Qin wrote: > > > Hi there, > > > I met the problem when I ran "grompp", the errors are: > > > ERROR 1 [file "po4lig4tip3.top ", line 26741]: > > > virtual site H21 (Res LG4-173) has non-zero mass 1.008 > > > Check your topology. > > > > > > ERROR 2 [file "po4lig4tip3.top", line 26741]: > > > virtual site H22 (Res LG4-173) has non-zero mass 1.008 > > > Check your topology. > > > > > > Then I checked my topology file, here were the definition of > > > LG4-173 H21 and H22: ( I want to convert the dummy atoms to H > atoms) > > > ;nr type resnr residue atom cgnr charge > > > mass type_B charge_B mass_B > > > 21 opls_999 1 LG4 H21 21 0.0000 > > > 1.00800 opls_172 0.4650 1.00800 > > > 22 opls_999 1 LG4 H22 22 0.0000 > > > 1.00800 opls_172 0.4650 1.00800 > > > > > > in which opls_999 was from what I defined by myself in the > > > force field itp file: > > > opls_999 DUM 0 1.008000 0.000 V 0.000000 > > 0.000000 > > > > > > I changed the both of the mass_A to 0.00000, but that > > didn't help. > > > Does anyone have ideas on that? > > > Thank you very much. > > > > > > Regards, > > > Qin > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > <mailto:gmx-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 [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > <mailto:gmx-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 [EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > gmx-users mailing list gmx-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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list gmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php