Dear Justin, I am trying to make topology file for cellulose II. The monomer unit is glucose (residue type GLCA). I do the following:
pdb2gmx -f cellulose.gro I am getting the following error while using pdbgmx. "Fatal Error: Atom -O not found in residue 2 while adding improper" Atom type "O" is actually not part of the GLCA residue. Only atom type OA is part of GLCA residue. Do I need to modify the rtp entry to suit my system or does this error corresponds to something else ? Your help is appreciated. Thanks, Vishal On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul <[email protected]> wrote: > > > Vishal Agarwal wrote: > >> 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. >> >> > The "-O" is not an atom type, it indicates an oxygen atom of a previous > residue. It is still not clear what it is you're doing or what the actual > problem is. If you want a resolution, you'll have to do as Mark asked and > post your command line and the actual error message. Remember, you're > asking for free help - you have to make it easy for us to help you. > > -Justin > > Vishal >> >> >> On Sun, Feb 7, 2010 at 4:54 AM, Mark Abraham <[email protected]<mailto: >> [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] >> <mailto:[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] >> <mailto:[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 >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > 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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