It is not straightforward to use the AMBER forcefield with Gromacs. You need to edit your pdb-file to account for different atom/residue names used by AMBER as opposed to GROMOS forcefields. Detailed info is here: http://chemistry.csulb.edu/ffamber/
If this is your first MD simulation, try things with one of the Gromos forcefields first. Andreas > -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of [email protected] > Sent: 29 May 2009 10:21 > To: [email protected] > Subject: [gmx-users] missing atoms > > Hi All, > > I am running Gromacs for drug enzyme complex using AMBER as > forcefield.While running pdb2gmx command I am getting error and warning of > 790 missing atoms. Can anybody suggest me how to correct this error. > > error : > ----------------------------------------------------------- > WARNING: atom H is missing in residue CYSH 703 in the pdb file > You might need to add atom H to the hydrogen database of residue > CYSH > in the file ff???.hdb (see the manual) > > > WARNING: atom HA is missing in residue CYSH 703 in the pdb file > You might need to add atom HA to the hydrogen database of residue > CYSH > in the file ff???.hdb (see the manual) > > > WARNING: atom HB1 is missing in residue CYSH 703 in the pdb file > You might need to add atom HB1 to the hydrogen database of > residue CYSH > in the file ff???.hdb (see the manual) > > > WARNING: atom HB2 is missing in residue CYSH 703 in the pdb file > You might need to add atom HB2 to the hydrogen database of > residue CYSH > in the file ff???.hdb (see the manual) > > ------------------------------------------------------- > Program pdb2gmx_mpi, VERSION 3.3.1 > Source code file: pdb2top.c, line: 697 > > Fatal error: > There were 790 missing atoms in molecule Protein_A, if you want to use > this incomplete topology anyhow, use the option -missing > ------------------------------------------------------- > > > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected] 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
