Hi Maik, I really did mix up a dummy atom with a virtual site. Any difference? Thank you very much for your help.
Regards, Qin On 9/12/07, Maik Goette <[EMAIL PROTECTED]> wrote: > > The problem actually is, that you mixed up a dummy atom with a virtual > site, I guess. > > Virtual sites are not allowed to have a mass, as the error message > claims. Also, a proper hydrogen should have a mass. > > If you want a hydrogen to appear, you have to place a particle in > A-state which has no non-bonded interaction, i.e. LJ & QQ interactions > should be zero. If you want to prevent it from flying away, you should > put bonded terms to the particle. > In the B-state, the QQ and LJ should be there (whereas the LJ > interaction for a hydrogen is 0 anyway). > > 21 opls_999 1 LG4 H21 21 0.0000 1.00800 > opls_172 0.4650 1.00800 > > opls_999 DUM 0 1.008000 0.000 A 0.000000 0.000000 > > So, I expect, this is, how it should look like. > Be aware of the missing bonded terms in the force field for a DUM > particle. Maybe, you want to call it H instead... > > Regards > > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > 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 > > 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 >
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