Hi Justin, Thanks a lot for the suggestions regarding the force field and the sulphide bond. The bond is now formed after changing the distance range in specbond.dat. Thanks. Sarada > > Message: 2 > Date: Wed, 26 Nov 2008 07:21:37 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Re: 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: >> 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. > > One piece of general advice - don't use ffgmx. It has long been > deprecated > (according to the manual, the output of pdb2gmx, and dozens of posts on > this > list). Use one of the newer Gromos96 force fields. > > Now, to address the actual question :) The only thing I can think of is > that > specbond.dat uses a simple distance search to determine if the atoms are > bonded, > and I believe the tolerance is something like 10%. So the value in > specbond.dat > of 0.25 implies that pdb2gmx should expect the S and Fe atoms to be 0.25 > +/- 0.2 > nm apart. If they are much further apart, no bond will be detected. > Check your > input .pdb file to see how far apart these two atoms are. > > -Justin > >> 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. 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 > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Wed, 26 Nov 2008 07:25:07 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Re: 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 > > > > Justin A. Lemkul wrote: > >> S and Fe atoms to be 0.25 +/- 0.2 nm apart. If they are much further > > Edit that: 0.25 nm +/- 0.02 nm. Apparently my math (and/or typing) skills > are > suspect first thing in the morning :) > > -Justin > > -- > ======================================== > > 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
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