Dear Justin, Thanks for replying. I really appreciate this.
Thanks, Vishal On Sun, Feb 7, 2010 at 3:58 PM, Justin A. Lemkul <[email protected]> wrote: > > > Vishal Agarwal wrote: > >> Dear Justin, >> >> Thanks for replying. I guess it should be -O4 from the convention but have >> to look more deeply to figure out that. >> I am noticing a few more things in the ffG45a3.rtp, entries like +N in the >> bonds and angles section. Since there is no atom type N in the monomer, are >> these entries correct or another typo ? >> >> > Probably another typo, unless glucose suddenly contains nitrogen and no one > notified the scientific community :) I would again suggest modifying the > .rtp entry (in a local copy of the .rtp file), modeled after ffG53a6.rtp, > since it appears to be more reliable. There is no need to alter the [atoms] > section, but it appears some of the bonded directives need some work. > > -Justin > > Vishal >> >> >> >> On Sun, Feb 7, 2010 at 1:18 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Vishal Agarwal wrote: >> >> 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. >> >> >> Not to my knowledge. As long as all of the expected atoms are >> there, you shouldn't have a problem. >> >> >> >> 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 ? >> >> >> The problem comes from this line in ffG45a3.rtp: >> >> [ impropers ] >> ; ai aj ak al gromos type >> C1 O5 -O C2 gi_2 >> >> Clearly the force field is expecting to assign an improper around >> carbon C1 using an "O" atom in a previous unit as a reference. I >> think this may be a typo in the file. The ffG53a6.rtp file has this >> line for the same improper: >> >> C1 O5 O1 C2 gi_2 >> >> I think this is what was intended. I do not know why the anomeric >> carbon would be using a previous residue as a reference for >> assigning an improper. Perhaps this is a bug. Make a local copy of >> ffG45a3.rtp and fix the line to make it look like the ffG53a6.rtp >> entry. Please report back if this works; it may need to be fixed >> for a future release. >> >> -Justin >> >> >> 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]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[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]>> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[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] >> >> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[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/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]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[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> <http://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]> >> <mailto:[email protected] <mailto:[email protected] >> >> >> <mailto:[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/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]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[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> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- 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
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