Dear Mark, What I meant over here is the missing oxygen (-O) which pdbgmx complains about is not a part of .rtp entry. There is no such type of oxygen specified in any of the .atp entry of the forcefield I am using.
Vishal On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham <[email protected]>wrote: > On 07/02/10 14:52, Vishal Agarwal wrote: > >> Dear All, >> >> Can anyone help me how can I go about preparing the topology file for an >> infinite crystal of cellulose. I have prepared the .gro file for 5X5X5 >> unit cells of cellulose II using GROMACS utility and intend to apply >> periodic BC on it. It has a glucose molecule as building block (GCLA). >> When I try running pdbgmx, I get an error for extra hydrogens (which is >> not there in itp file but is actually there in the original structure >> which I am using) and missing oxygen (-O). >> > > People who might help aren't at all interested in your description of the > error message. If the contents of your head were reliable, you wouldn't have > seen the error in the first place, or would have solved the issue already. > :-) Copy and paste your command line, and what seems to be the relevant part > of the error. > > To use pdb2gmx, you need .rtp file entries that correspond to your > monomers. If not, you will not be able to use pdb2gmx to generate your > topology files. > > Mark > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Regards *********************************************** Vishal Agarwal Research Scholar University of Massachusetts, Amherst *********************************************** 'Your only obligation in any lifetime is to be true to yourself." ---Richard Bach
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