Dear Justin, Thanks for replying.
pdb2gmx -f cellulose.gro >> >> > So then your "cellulose.gro" contains all the atoms of GLCA monomers, named > exactly as the force field expects them? Have you checked against the .rtp > entry? What force field are you using? > > ;; > Should they be exactly in the same order as the rtp entry ? The atom type I specified is definitely according to the standard convention of rtp entry. I am using G45a3 as the force field. >> 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. >> > > pdb2gmx is complaining about an atom, not an atom type. Somewhere in the > .rtp file (probably within the [impropers] section, there should be a line > specifying an atom named O that belongs to the preceding residue (hence the > minus sign). None of my .rtp files are like this. Did you create a custom > .rtp entry? > > ;; No I didnt create a custom rtp entry. > > Do I need to modify the rtp entry to suit my system or does this error >> corresponds to something else ? >> >> > That will depend upon the answers to the above questions. If you created > the .rtp entry, then you'll have to fix the problem of naming mismatch. If > you're using the standard .rtp entry for the force field, then it's easier > to modify your coordinate file to match the naming expected by the force > field. > > ;; The problem I am having is where to modify my coordinate file. The residue doesnot contain a atom type 'O'. Another curious question I have is suppose if I have another system where the a monomer uint say GLCA (specified in rtp) is connected by a bridging atom say Carbon. Do I need to create a new rtp entry for pdbgmx to work or is there a work around by specifying that carbon as a separate residue ? Again thanks for replying. Best, Vishal -Justin > > Your help is appreciated. >> Thanks, >> Vishal >> >> On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul <[email protected]<mailto: >> [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]> >> <mailto:[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]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> -- 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
-- 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
