Dear Abdul, I had a similar error always with residue number 2 when using the amber ports in gromacs. Manually adding the hydrogen to the backbone nitrogen that connects to residue 1 will fix this.
You might know how to do this but just in case here is how I do it: load your pdb into any builder and add the hydrogen into a reasonable position(i.e no steric clash) on the nitrogen. write out a pdb. I find that builders can change the format of pdb's so I usually just copy the H line and add it into my original pdb formatting it as needed. It is the only H that needs to be defined. pdb2gmx will take care of the rest. I'm not sure why this happens but I didn't look too much into it at the time as I was learning how to use gromacs and everything was going wrong :) Hope this helps, Oliver On 3 July 2010 16:50, Carsten Kutzner <ckut...@gwdg.de> wrote: > Dear Abdul, > > please keep all Gromacs-related questions on the mailing list. > > Best, > Carsten > > > > Begin forwarded message: > > *From: *"abdul wadood" <wadoodbiochem...@hotmail.com> > *Date: *July 3, 2010 8:40:29 AM GMT+02:00 > *To: *<ckut...@gwdg.de> > *Subject: **missing atom* > > Dear Carsten > > I am running simulation using gromacs with amber forcefields on my protein. > I have prepared the input file accordingly and have all the required > library. But the problem is that when i run pdb2gmx for the top file the > following error come: > > WARNING: atom H is missing in residue LEU 2 in the pdb file > You might need to add atom H to the hydrogen database of residue > LEU > in the file ff???.hdb > > I tried my best to solve the problem, searching on the gromacs website and > manual but cannot succeed. > If you kindly help me in this respect your help will be highly appreciated > by our group our research. > the input file is attached. > > Many regards > > Abdul Wadood, > Research Scholar, > Dr.Panjwani Center for Molecular Medicine and > Drug Research, > International Center for Chemical and > Biological Science, > University of Karachi, Karachi-75720, Pakistan. > Email:wadoodbiochem...@hotmail.com > > > > > > > -- > 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 >
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