Hi Justin, Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said the topology file does contain the bonds and I need not have made the modificatins to specbond.dat. But using the original specbond.dat does not prevent the protonation of CYS. I renamed CYS as CYS2 in the input pdb file and used the following command line pdb2gmx_mpi -ignh -ff gmx -f 2c9_s50.pdb -o protein_h.pdb -p topology.top -water spce Am I missing some crucial option here (like -ss for disulphide bonds)? Thanks once again. Regards, Sarada
> Message: 6 > Date: Tue, 25 Nov 2008 07:17:14 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > [EMAIL PROTECTED] wrote: >> Hello, >> Sorry, I realised the HEME HEC naming was not the problem. But still the >> pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets >> protonated and doesnot form a bond with HEME. I tried to preserve the >> bonds by editing the specbond.dat file. I do not know if it can be used >> for intramolecular bonding. Kindly inform if the modifications I have >> made >> are valid. The runtime information during the execution of pdb2gmx >> indicated the linking of FE in HEME to the N atoms. However, I do not >> see >> the bonds when I open the output file in Pymol. Please indicate how this >> problem can be resolved. >> > > Well, using visualization software may not indicate anything. Most > programs > decide on bonds based on distance, not any sort of intelligent mechanism. > The > question is whether or not these bonds show up in your topol.top. > >> This is the content of my specbond.dat file: >> >> 5 >> CYS SG 1 HEME FE 5 0.25 CYS HEME > > Well, this may be why your Cys is getting protonated - you're telling > pdb2gmx > that it should be! See the format of specbond.dat here: > > http://wiki.gromacs.org/index.php/specbond.dat > > The second-to-last column should be the new residue name for cysteine, > probably > you want something like CYS2. > >> HEME FE 5 HEME NA 3 0.22 HEME HEME >> HEME FE 5 HEME NB 3 0.22 HEME HEME >> HEME FE 5 HEME NC 3 0.22 HEME HEME >> HEME FE 5 HEME ND 3 0.22 HEME HEME >> > > Why is this section (above) even necessary? Are these bonds not defined > in the > .rtp file of your force field? Which force field are you using? I know > these > are defined in the Gromos-type force fields. > > Try again with the original specbond.dat, but don't assume that > visualization > software will always indicate the presence/absence of a bond. Examine > your > topology for that. > > -Justin > >> And these I obtained during the execution of pdbgmx: >> >> Opening library file specbond.dat >> 5 out of 5 lines of specbond.dat converted succesfully >> Special Atom Distance matrix: >> CYS122 CYS135 CYS143 CYS146 CYS150 CYS237 CYS309 >> SG958 SG1059 SG1118 SG1136 SG1165 SG1902 SG2475 >> CYS135 SG1059 1.677 >> CYS143 SG1118 1.076 1.092 >> CYS146 SG1136 1.313 1.792 0.749 >> CYS150 SG1165 1.175 2.054 0.978 0.426 >> CYS237 SG1902 2.194 3.510 2.536 1.933 1.632 >> CYS309 SG2475 1.745 2.703 2.469 2.507 2.423 2.449 >> CYS343 SG2748 4.679 4.998 4.364 3.763 3.870 3.329 4.426 >> CYS406 SG3265 2.258 2.657 2.051 1.603 1.744 1.886 2.198 >> CYS457 SG3657 2.232 0.829 1.894 2.582 2.825 4.173 2.898 >> HEME462 FE3693 2.257 2.566 1.949 1.489 1.669 1.956 2.343 >> HEME462 NA3694 2.456 2.680 2.110 1.663 1.862 2.118 2.486 >> HEME462 NB3695 2.199 2.426 1.883 1.498 1.704 2.088 2.247 >> HEME462 NC3696 2.061 2.462 1.795 1.321 1.479 1.809 2.217 >> HEME462 ND3697 2.331 2.711 2.031 1.505 1.657 1.841 2.455 >> CYS343 CYS406 CYS457 HEME462 HEME462 HEME462 HEME462 >> SG2748 SG3265 SG3657 FE3693 NA3694 NB3695 NC3696 >> CYS406 SG3265 2.501 >> CYS457 SG3657 5.547 3.210 >> HEME462 FE3693 2.512 0.219 3.147 >> HEME462 NA3694 2.361 0.325 3.240 0.211 >> HEME462 NB3695 2.647 0.293 2.977 0.208 0.295 >> HEME462 NC3696 2.671 0.286 3.064 0.209 0.420 0.297 >> HEME462 ND3697 2.389 0.314 3.318 0.208 0.297 0.416 0.293 >> >> >> Linking HEME-462 FE-3693 and HEME-462 NA-3694... >> Linking HEME-462 FE-3693 and HEME-462 NB-3695... >> Linking HEME-462 FE-3693 and HEME-462 NC-3696... >> Linking HEME-462 FE-3693 and HEME-462 ND-3697... >> N-terminus: PRO-NH2+ >> C-terminus: COO- >> Now there are 462 residues with 4749 atoms >> Making bonds... >> >> Thanks. >> Sarada >> Graduate Student, >> NCBS, Bangalore >> >> >> >> >> Hello, >> I am working with the simulation of cytochromeP450. In the output of the >> pdb2gmx command, the iron atom in the HEME loses all the bonds, >> including >> the sulphide bond with cystine. Also, the command changed the residue >> name >> from HEME to HEC. During the execution of the pdb2gmx, I get this >> warning: >> >> Warning: 'HEC' not found in residue topology database, trying to use >> 'HEME' >> >> Can someone please tell me, if this is responsible for the loss of bonds >> especially the one between CYS and FE. How can the bonds be retained? >> Thanks. >> Sarada >> >> >> >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.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 >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > 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@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 55, Issue 132 > ****************************************** > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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. 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