[gmx-users] Re: gmx-users Digest, Vol 56, Issue 43
Dear Art, Thanks a lot for the reference. Regards, Sarada >> Message: 5 > Date: Fri, 12 Dec 2008 19:21:02 -0800 > From: Arthur Roberts > Subject: Re: [gmx-users] [Fwd: Loss of bonds in HEME iron after > pdb2gmx] > To: Discussion list for GROMACS users > Message-ID: <81b152bc-bb35-4cf2-a9e5-736c20e89...@yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Dear Sarada, > > You need to paramterize the Cysteinyl ligand manually. There are a > variety of references in the literature that provide reasonable > energies. Below is a pretty good reference. > > Best wishes, > Art > > 1.Oda, A., Yamaotsu, N., and Hirono, S. (2005) New AMBER force field > parameters of heme iron for cytochrome P450s determined by quantum > chemical calculations of simplified models, J. Comput. Chem. 26, > 818-826. > > > On Dec 9, 2008, at 10:59 PM, sara...@ncbs.res.in wrote: > >> Hello, >> I am working with the simulation of cytochromeP450. There is a bond >> between the S of cystine and FE of HEME. During the grompp step I get >> warnings that there is no default bonds/angles/dihedrals all >> pertaining to >> the cystine-heme bond. In the archives it was mentioned that these >> values >> must be taken from ffG**bon.itp and included in the topology file. >> However >> in the ffG**bon.itp file, the bonds/angles mentioned seem to be >> between S >> of CYS and the carbon atom of HEME. For eg, >> >> ; bond-, angle- and dihedraltypes for specbonds: >> [ bondtypes ] >> S S 2gb_33 >> NR FE 2gb_32 >> ; cystine - heme link (is CR1-S, use CH2-S): >> S CR1 2gb_30 >> >> Should not the cystine - heme link have FE insteadof CR1? I understand >> that I am missing some crucial point here. Kindly help. >> Thanks. >> Sarada >> Graduate student, >> NCBS, >> Bangalore ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] [Fwd: Loss of bonds in HEME iron after pdb2gmx]
Hello, I am working with the simulation of cytochromeP450. There is a bond between the S of cystine and FE of HEME. During the grompp step I get warnings that there is no default bonds/angles/dihedrals all pertaining to the cystine-heme bond. In the archives it was mentioned that these values must be taken from ffG**bon.itp and included in the topology file. However in the ffG**bon.itp file, the bonds/angles mentioned seem to be between S of CYS and the carbon atom of HEME. For eg, ; bond-, angle- and dihedraltypes for specbonds: [ bondtypes ] S S 2gb_33 NR FE 2gb_32 ; cystine - heme link (is CR1-S, use CH2-S): S CR1 2gb_30 Should not the cystine - heme link have FE insteadof CR1? I understand that I am missing some crucial point here. Kindly help. Thanks. Sarada Graduate student, NCBS, Bangalore ___ 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
[gmx-users] Re: Re: Loss of bonds in HEME iron after pdb2gmx
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 > 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 >>> 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 >>>
[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 > 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
[gmx-users] Loss of bonds in HEME iron after pdb2gmx
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. This is the content of my specbond.dat file: 5 CYS SG 1 HEMEFE 5 0.25CYS HEME HEMEFE 5 HEMENA 3 0.22HEMEHEME HEMEFE 5 HEMENB 3 0.22HEMEHEME HEMEFE 5 HEMENC 3 0.22HEMEHEME HEMEFE 5 HEMEND 3 0.22HEMEHEME 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 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
[gmx-users] location of specbond.dat-solved
Hello, The file in the local directory is the one that is considered. I am sorry for the previous mail. Regards, Sarada Graduate student, NCBS, Bangalore. Hello, > I am working in a cluster environment and so, all files there including > specbond.dat file are write protected. Can someone indicate how I can > specify that the program must consider the modified file (specbond.dat) in > my local working directory rather than the one in the main directory? > Thanks. > Sarada > ___ 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
[gmx-users] location of specbond.dat
Hello, I am working in a cluster environment and so, all files there including specbond.dat file are write protected. Can someone indicate how I can specify that the program must consider the modified file (specbond.dat) in my local working directory rather than the one in the main directory? Thanks. Sarada ___ 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
[gmx-users] Loss of bonds in HEME iron after pdb2gmx
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 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
