Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx
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 ___ gmx-users mailing listgmx-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
Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx
[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 HEMEFE 5 0.25CYS 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. HEMEFE 5 HEMENA 3 0.22HEMEHEME HEMEFE 5 HEMENB 3 0.22HEMEHEME HEMEFE 5 HEMENC 3 0.22HEMEHEME HEMEFE 5 HEMEND 3 0.22HEMEHEME 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
[gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx
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 HEMEFE 5 0.25CYS 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. HEMEFE 5 HEMENA 3 0.22HEMEHEME HEMEFE 5 HEMENB 3 0.22HEMEHEME HEMEFE 5 HEMENC 3 0.22HEMEHEME HEMEFE 5 HEMEND 3 0.22HEMEHEME 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
