sorry about the previous post! I have not yet looked at the code for pdb2gmx (and a lot of other stuff). I think the formyl-valine idea is pretty cool and found this thread very informative. Thank you! Shounak
Justin A. Lemkul wrote > > On 6/27/12 2:49 PM, shounakb wrote: >> Hi Shima, >> i do not think pdb2gmx uses the tdb files. However, I feel that the >> FOR >> tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb >> > > Both of these assertions are incorrect. The *only* Gromacs program that > uses > .tdb files is pdb2gmx. The FOR cap is on the N-terminus, so it cannot be > in > .c.tdb. Both .tdb files are irrelevant for this problem, as stated > before. > >> I saw your other thread where you have described the FOR topology you >> added. >> I think the atoms should be CA and O and their respective atom types, >> CH1/CH2 and O. >> > > This does not solve the problem. If one changes the "C" atom name to "CA" > then > pdb2gmx will certainly complain that the atom "C" is missing, since > improper > construction for VAL is dependent upon atoms "C" and "CA" being present in > the > preceding residue. > >> I guess you already have partial charges for the atoms? Shouldn't that >> solve >> the problem with VAL that Justin highlighted, without having to comment >> out >> the impropers line? >> > > Partial charges are irrelevant here. The error complains about an atom > not > being found, not the charge on any given atom. Shima has a functional > .rtp > entry for the FOR residue. It is not the problem, VAL is. Better stated, > the > mechanism used by gmx.ff to generate impropers in this case blocks the use > of > FOR as a separate residue, since it does not contain the same atoms as an > amino > acid, specifically a C and CA. > > -Justin > >> Regards, >> Shounak >> >> >> Shima Arasteh wrote >>> >>> :)) >>> I can't eliminate it, I decided to do , but when I studied about the >>> structure of protein ( consists of 2 monomers, which form a dimer in >>> lipid >>> bilayer, and the reason of this formation is the existence of formyl >>> residues in N-teminals) . Then I got regretful to remove it. Don't you >>> agree? >>> >>> >>> Sincerely, >>> Shima >>> >>> >>> ----- Original Message ----- >>> From: Justin A. Lemkul <jalemkul@> >>> To: Discussion list for GROMACS users <gmx-users@> >>> Cc: >>> Sent: Wednesday, June 27, 2012 10:25 PM >>> Subject: Re: [gmx-users] Re: pdb2gmx error >>> >>> >>> >>> On 6/27/12 1:52 PM, shounakb wrote: >>>> Shima, I use gromacs-4.5.4. Without the FOR residue, my >>>> gmx.ff/aminoacids.rtp >>>> file works fine for the sequence you originally specified. (pdb2gmx >>>> executes >>>> without any errors) >>>> I guess you added the FOR cap's topology yourself? >>>> >>>> Justin, could this be an issue? >>>> >>> >>> Please see the previous posts on these topics, including the post from >>> just a few minutes ago where I discovered the source of the problem. >>> The >>> FOR residue issue has been an ongoing discussion over several weeks. I >>> will maintain that I do not necessarily believe that a two-atom model of >>> a >>> formyl group is sufficiently accurate for a Gromos force field, since >>> the >>> alpha proton is very polar and thus may need to be explicitly >>> represented. I have stated my skepticism before but it appears Shima is >>> pursuing the current course. Side note ;) >>> >>> -Justin >>> >>> -- ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> 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 gmx-users@ >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Only plain text messages are allowed! >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-request@. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> -- >>> gmx-users mailing list gmx-users@ >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Only plain text messages are allowed! >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-request@. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> -- >> View this message in context: >> http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998870.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 gmx-users@ > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request@. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998875.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
