Re: [gmx-users] Using specbond.dat in pdb2gmx
Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. Okay, which file do I remove the N and C prefixes from? Coordinate file, always manipulate the coordinate file. But the fact that you're asking this tells me that likely you never actually added those prefixes, so pdb2gmx is being smart and adding them for you. In that case, there's nothing you can do short of (1) modifying the pdb2gmx code, (2) manually hacking the topology - ugly, but effective, or (3) using a different force field that doesn't have terminus-specific naming (anything that's not Amber). After discussing it with my professor, he believes that I can attempt both (2) and (3) until one of them works. Currently, he and I are going through the process of designing a script to perform (2). Additionally, he told me that the only forcefields other than amber99sb that I can try are charmm27 and opls-aa. However, when I attempted to use either of those forcefields (these times I was relieved to finally see the option to select none for the termini), I received this error message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Does this have to do with the fact that I did select none for both terminals both of the times? Matthew -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
(Ignore the earlier message) Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. Okay, which file do I remove the N and C prefixes from? Coordinate file, always manipulate the coordinate file. But the fact that you're asking this tells me that likely you never actually added those prefixes, so pdb2gmx is being smart and adding them for you. In that case, there's nothing you can do short of (1) modifying the pdb2gmx code, (2) manually hacking the topology - ugly, but effective, or (3) using a different force field that doesn't have terminus-specific naming (anything that's not Amber). After discussing it with my professor, he believes that I can attempt both (2) and (3) until one of them works. Currently, he and I are going through the process of designing a script to perform (2). Additionally, he told me that the only forcefields other than amber99sb that I can try are charmm27 and opls-aa. However, when I attempted to use either of those forcefields (these times I was relieved to finally see the option to select none for the termini), I received this error message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Does this have to do with the fact that I did select none for both terminals both of the times? Here is the full command line: pdb2gmx_mpi -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter And because I do not want to leave any information out, here is the full text for each of these (the difference between the two forcefields being the selection of the respective forcefields): __ :-) pdb2gmx_mpi (-: Option Filename Type Description -f 1NB1.pdb InputStructure file: gro g96 pdb tpr etc. -o conf.gro Output Structure file: gro g96 pdb etc. -p topol.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsepenum id_or_ter Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id or interactive -merge enum no Merge multiple chains into a single [moleculetype]: no, all or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum tip3p Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool yes Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, instead of charged (default) -[no]lys bool no Interactive lysine selection, instead of charged -[no]arg bool no Interactive arginine selection, instead of charged -[no]asp bool no Interactive aspartic acid selection, instead of charged -[no]glu bool no Interactive glutamic acid selection, instead of charged -[no]gln bool no Interactive glutamine selection, instead of neutral -[no]his bool no Interactive histidine selection, instead of checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the coordinate file
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/19/14, 3:00 PM, Matthew Stancea wrote: (Ignore the earlier message) Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. Okay, which file do I remove the N and C prefixes from? Coordinate file, always manipulate the coordinate file. But the fact that you're asking this tells me that likely you never actually added those prefixes, so pdb2gmx is being smart and adding them for you. In that case, there's nothing you can do short of (1) modifying the pdb2gmx code, (2) manually hacking the topology - ugly, but effective, or (3) using a different force field that doesn't have terminus-specific naming (anything that's not Amber). After discussing it with my professor, he believes that I can attempt both (2) and (3) until one of them works. Currently, he and I are going through the process of designing a script to perform (2). Additionally, he told me that the only forcefields other than amber99sb that I can try are charmm27 and opls-aa. However, when I attempted to use either of those forcefields (these times I was relieved to finally see the option to select none for the termini), I received this error message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Does this have to do with the fact that I did select none for both terminals both of the times? Yes, because pdb2gmx has difficulty figuring out that your termini have full valences on each of the atoms in the peptide bond. Special bonds and .rtp bonds are handled separately. If your input structure has all of the necessary hydrogen atoms (named correctly), then you *might* be able to get away with using the -missing flag. This is not something that is normally recommended, and it is potentially dangerous. Any topology generated with -missing should be scrutinized heavily to make sure everything is right. I can only think of one other constructive use of -missing, so be advised (and this goes for anyone else who comes across this post) that this is generally a very bad idea, so don't try to apply it in any other case. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. ie. do the replacement on your input coordinate file, not the .rtp! Mark Dr. Mark Abraham, My pdb file contains HB1 and HB2 on a beta carbon of a cysteine. Well, connected to that carbon (other than the alpha carbon) is the sulfur molecule. The only logical placement of for HB3 is to that sulfur, except that the sulfur should not have any hydrogens bound to it since it is supposed form a disulfide bridge with another cysteine. Because of that, I am sure you can understand why I am scratching my head on this issue... HB3 is sometimes the nomenclature of beta carbons (some programs write HB2 and HB3 instead of HB1 and HB2, and the B means beta). Your description doesn't make any real sense to me. Visualize your structure. If you have a full set of protons on Cys, you should have HA, HB1, and HB2 on the side chain to make the force field happy. If there is an HG on SG (the sulfur atom), then it will be deleted by pdb2gmx when you tell it to create a disulfide. -Justin My apologies! My description was not very clear, and now I see that. However, because you mentioned that HG would be the name of the hydrogen attached to the sulfur, I believe that perhaps changing the name of some of the hydrogens in the pdb file can fix the issue. After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. However, even with this small discrepancy, I am astounded that I was able to finally generate a conf.gro and topol.top of a cyclotide with a bond between the terminal N and the terminal C! Thank you so much for your help, Dr. Lemkul and Dr. Abraham! Matthew -Matthew Stancea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/18/14, 3:31 PM, Matthew Stancea wrote: Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. ie. do the replacement on your input coordinate file, not the .rtp! Mark Dr. Mark Abraham, My pdb file contains HB1 and HB2 on a beta carbon of a cysteine. Well, connected to that carbon (other than the alpha carbon) is the sulfur molecule. The only logical placement of for HB3 is to that sulfur, except that the sulfur should not have any hydrogens bound to it since it is supposed form a disulfide bridge with another cysteine. Because of that, I am sure you can understand why I am scratching my head on this issue... HB3 is sometimes the nomenclature of beta carbons (some programs write HB2 and HB3 instead of HB1 and HB2, and the B means beta). Your description doesn't make any real sense to me. Visualize your structure. If you have a full set of protons on Cys, you should have HA, HB1, and HB2 on the side chain to make the force field happy. If there is an HG on SG (the sulfur atom), then it will be deleted by pdb2gmx when you tell it to create a disulfide. -Justin My apologies! My description was not very clear, and now I see that. However, because you mentioned that HG would be the name of the hydrogen attached to the sulfur, I believe that perhaps changing the name of some of the hydrogens in the pdb file can fix the issue. After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. You need to be using -ter and choosing None for both termini, otherwise the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. You need to be using -ter and choosing None for both termini, otherwise the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. -Justin I used the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter and was asked about the protonation states for two of the residues, but I was not asked about the termini. -Matthew -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/18/14, 4:53 PM, Matthew Stancea wrote: After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. You need to be using -ter and choosing None for both termini, otherwise the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. -Justin I used the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter and was asked about the protonation states for two of the residues, but I was not asked about the termini. Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 With the above specbond.dat file in the working directory, I attempted the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp and received this fatal error message (it is the same as the original): --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your input coordinate file does not conform to the required nomenclature of the force field. The error message says it all. So according to the error message, it says that I can remove the HB3 from the rtp entry NCYX. I was able to locate that to at least one file: residues.xml. Will editing that file (while backing up the original of course) allow me to bypass this error? For example, if I manually edit that file so that rtp entry NCYX contains all the atoms and only the atoms I want my initial atom to have, can pdb2gmx use that file in that way? Thanks again! -Matthew Stancea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/17/14, 1:51 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 With the above specbond.dat file in the working directory, I attempted the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp and received this fatal error message (it is the same as the original): --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your input coordinate file does not conform to the required nomenclature of the force field. The error message says it all. So according to the error message, it says that I can remove the HB3 from the rtp entry NCYX. I was able to locate that to at least one file: residues.xml. Will editing that file (while backing up the original of course) allow me to bypass this error? For example, if I manually edit that file so that rtp entry NCYX contains all the atoms and only the atoms I want my initial atom to have, can pdb2gmx use that file in that way? No, absolutely not. You should never modify the force field files in such a way. The force field has expected nomenclature. You must make your coordinate file match that nomenclature, not the other way around. If you start removing atoms from the .rtp file, your whole setup will be junk. The simple answer here has already been printed by pdb2gmx. Use -ignh to have the H atoms built back onto the structure and magically named correctly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. Mark On Tue, Jun 17, 2014 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/17/14, 1:51 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 With the above specbond.dat file in the working directory, I attempted the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp and received this fatal error message (it is the same as the original): --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your input coordinate file does not conform to the required nomenclature of the force field. The error message says it all. So according to the error message, it says that I can remove the HB3 from the rtp entry NCYX. I was able to locate that to at least one file: residues.xml. Will editing that file (while backing up the original of course) allow me to bypass this error? For example, if I manually edit that file so that rtp entry NCYX contains all the atoms and only the atoms I want my initial atom to have, can pdb2gmx use that file in that way? No, absolutely not. You should never modify the force field files in such a way. The force field has expected nomenclature. You must make your coordinate file match that nomenclature, not the other way around. If you start removing atoms from the .rtp file, your whole setup will be junk. The simple answer here has already been printed by pdb2gmx. Use -ignh to have the H atoms built back onto the structure and magically named correctly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
ie. do the replacement on your input coordinate file, not the .rtp! On Tue, Jun 17, 2014 at 10:35 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. Mark On Tue, Jun 17, 2014 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/17/14, 1:51 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 With the above specbond.dat file in the working directory, I attempted the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp and received this fatal error message (it is the same as the original): --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your input coordinate file does not conform to the required nomenclature of the force field. The error message says it all. So according to the error message, it says that I can remove the HB3 from the rtp entry NCYX. I was able to locate that to at least one file: residues.xml. Will editing that file (while backing up the original of course) allow me to bypass this error? For example, if I manually edit that file so that rtp entry NCYX contains all the atoms and only the atoms I want my initial atom to have, can pdb2gmx use that file in that way? No, absolutely not. You should never modify the force field files in such a way. The force field has expected nomenclature. You must make your coordinate file match that nomenclature, not the other way around. If you start removing atoms from the .rtp file, your whole setup will be junk. The simple answer here has already been printed by pdb2gmx. Use -ignh to have the H atoms built back onto the structure and magically named correctly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. ie. do the replacement on your input coordinate file, not the .rtp! Mark Dr. Mark Abraham, My pdb file contains HB1 and HB2 on a beta carbon of a cysteine. Well, connected to that carbon (other than the alpha carbon) is the sulfur molecule. The only logical placement of for HB3 is to that sulfur, except that the sulfur should not have any hydrogens bound to it since it is supposed form a disulfide bridge with another cysteine. Because of that, I am sure you can understand why I am scratching my head on this issue... -Matthew Stancea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/17/14, 4:43 PM, Matthew Stancea wrote: Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. ie. do the replacement on your input coordinate file, not the .rtp! Mark Dr. Mark Abraham, My pdb file contains HB1 and HB2 on a beta carbon of a cysteine. Well, connected to that carbon (other than the alpha carbon) is the sulfur molecule. The only logical placement of for HB3 is to that sulfur, except that the sulfur should not have any hydrogens bound to it since it is supposed form a disulfide bridge with another cysteine. Because of that, I am sure you can understand why I am scratching my head on this issue... HB3 is sometimes the nomenclature of beta carbons (some programs write HB2 and HB3 instead of HB1 and HB2, and the B means beta). Your description doesn't make any real sense to me. Visualize your structure. If you have a full set of protons on Cys, you should have HA, HB1, and HB2 on the side chain to make the force field happy. If there is an HG on SG (the sulfur atom), then it will be deleted by pdb2gmx when you tell it to create a disulfide. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 With the above specbond.dat file in the working directory, I attempted the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp and received this fatal error message (it is the same as the original): --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -Matthew Stancea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/16/14, 12:31 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 With the above specbond.dat file in the working directory, I attempted the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp and received this fatal error message (it is the same as the original): --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your input coordinate file does not conform to the required nomenclature of the force field. The error message says it all. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Dr. Justin Lemkul, Now I understand the message about removal of bonds being just duplicate bonds that have been removed, and, also, I understand how the -ter flag works now. This is the screen output related to parsing of specbond.dat: 3 out of 3 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS1CYS1CYS5CYS5VAL6 CYS10 CYS10 N1 SG6 N47SG52 C59N101 SG106 CYS1 SG6 0.302 CYS5 N47 0.988 0.900 CYS5SG52 1.070 0.917 0.333 VAL6 C59 1.498 1.396 0.510 0.585 CYS10N101 1.122 0.901 0.614 0.609 0.835 CYS10 SG106 0.879 0.655 0.490 0.422 0.857 0.322 CYS15N160 0.784 0.488 1.066 0.984 1.477 0.774 0.620 CYS15 SG165 0.477 0.202 0.960 0.961 1.432 0.823 0.625 CYS17N184 1.030 0.784 0.721 0.460 1.004 0.617 0.387 CYS17 SG189 1.224 1.039 0.514 0.204 0.625 0.621 0.487 VAL21C245 0.756 0.685 0.408 0.388 0.847 0.812 0.531 CYS22N259 0.657 0.574 0.404 0.432 0.887 0.742 0.458 CYS22 SG264 0.755 0.588 0.371 0.430 0.827 0.436 0.203 VAL29C363 0.132 0.394 1.117 1.193 1.626 1.248 1.004 Here is precisely why your specbond.dat is not working - the bond criteria are not satisfied. The Cys1(N)-Val29(C) distance is 0.132 nm. You're specifing in specbond.dat (likely from simply copying the contents of the other lines) that the reference distance is 0.25 nm. If Gromacs does not find atoms within ±10% of the value in specbond.dat, a bond won't be created. Since 0.132 nm is way off, you won't get a bond. Also note that your final columns will try to rename the residues to CYS2 (which is specific for a disulfide cysteine, so unless that's true you'll get more fatal errors) and VAL2, which doesn't exist. See http://www.gromacs.org/Documentation/File_Formats/specbond.dat Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 -Matthew Stancea (This email chain has gotten a bit long in my opinion, so I have put the previous email below. With your permission, I would prefer just using the above message in order to continue correspondence in shorter emails; however, if you would prefer to instead use the entire email, I completely understand.) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, June 12, 2014 5:01 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Using specbond.dat in pdb2gmx On 6/12/14, 4:53 PM, Matthew Stancea wrote: On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the option -ignh at the end of my command, but doing so deletes the bond between the first nitrogen and the last carbon (which should be connected for this peptide to be cyclic) and adds two additional hydrogens and a positive charge to the first nitrogen and an additional oxygen and a negative charge to the last carbon, rendering this peptide as non-cyclic. After searching around for quite a while, I found out that many others on this mailing list were having the same issues as myself, and some replies to their messages including the usage of a file known as specbond.dat which may be helpful in retaining that bond. The -ignh flag is not relevant to those observations. In my working directory, I have a file named specbond.dat and it contains the following information: 3 CYS N 1 VAL C 1 0.25CYS2VAL2 CYS SG 1 CYS SG 1 0.25CYS2CYS2 CYM SG 1 CYM SG 1 0.25CYS2CYS2 When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp while specbond.dat is in the working directory (Here is a link for the structure of peptide 1NB1 for reference if needed: http://www.ncbi.nlm.nih.gov/protein/1NB1_A ), I get the following message: --- Program pdb2gmx_mpi
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/13/14, 12:57 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Now I understand the message about removal of bonds being just duplicate bonds that have been removed, and, also, I understand how the -ter flag works now. This is the screen output related to parsing of specbond.dat: 3 out of 3 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS1CYS1CYS5CYS5VAL6 CYS10 CYS10 N1 SG6 N47SG52 C59N101 SG106 CYS1 SG6 0.302 CYS5 N47 0.988 0.900 CYS5SG52 1.070 0.917 0.333 VAL6 C59 1.498 1.396 0.510 0.585 CYS10N101 1.122 0.901 0.614 0.609 0.835 CYS10 SG106 0.879 0.655 0.490 0.422 0.857 0.322 CYS15N160 0.784 0.488 1.066 0.984 1.477 0.774 0.620 CYS15 SG165 0.477 0.202 0.960 0.961 1.432 0.823 0.625 CYS17N184 1.030 0.784 0.721 0.460 1.004 0.617 0.387 CYS17 SG189 1.224 1.039 0.514 0.204 0.625 0.621 0.487 VAL21C245 0.756 0.685 0.408 0.388 0.847 0.812 0.531 CYS22N259 0.657 0.574 0.404 0.432 0.887 0.742 0.458 CYS22 SG264 0.755 0.588 0.371 0.430 0.827 0.436 0.203 VAL29C363 0.132 0.394 1.117 1.193 1.626 1.248 1.004 Here is precisely why your specbond.dat is not working - the bond criteria are not satisfied. The Cys1(N)-Val29(C) distance is 0.132 nm. You're specifing in specbond.dat (likely from simply copying the contents of the other lines) that the reference distance is 0.25 nm. If Gromacs does not find atoms within ±10% of the value in specbond.dat, a bond won't be created. Since 0.132 nm is way off, you won't get a bond. Also note that your final columns will try to rename the residues to CYS2 (which is specific for a disulfide cysteine, so unless that's true you'll get more fatal errors) and VAL2, which doesn't exist. See http://www.gromacs.org/Documentation/File_Formats/specbond.dat Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 -Matthew Stancea (This email chain has gotten a bit long in my opinion, so I have put the previous email below. With your permission, I would prefer just using the above message in order to continue correspondence in shorter emails; however, if you would prefer to instead use the entire email, I completely understand.) Snipping out relevant portions is perfectly fine (and preferred) as long as you don't nuke something actually important. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the option -ignh at the end of my command, but doing so deletes the bond between the first nitrogen and the last carbon (which should be connected for this peptide to be cyclic) and adds two additional hydrogens and a positive charge to the first nitrogen and an additional oxygen and a negative charge to the last carbon, rendering this peptide as non-cyclic. After searching around for quite a while, I found out that many others on this mailing list were having the same issues as myself, and some replies to their messages including the usage of a file known as specbond.dat which may be helpful in retaining that bond. The -ignh flag is not relevant to those observations. In my working directory, I have a file named specbond.dat and it contains the following information: 3 CYS N 1 VAL C 1 0.25CYS2VAL2 CYS SG 1 CYS SG 1 0.25CYS2CYS2 CYM SG 1 CYM SG 1 0.25CYS2CYS2 When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp while specbond.dat is in the working directory (Here is a link for the structure of peptide 1NB1 for reference if needed: http://www.ncbi.nlm.nih.gov/protein/1NB1_A ), I get the following message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYS with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- (HB3 would be the hydrogen of a cysteine residue that has not formed a disulfide bond with another amino acid residue, however my pdb does not contain an HB3). I then tried adding -ignh as per the suggestion in the twelfth line in that message. The following is a part of the message I received: Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 29 residues with 385 atoms Making bonds... Number of bonds was 390, now 389 Generating angles, dihedrals and pairs... Before cleaning: 1010 pairs Before cleaning: 1030 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 1030 dihedrals, 73 impropers, 699 angles 1007 pairs, 389 bonds and 0 virtual sites Total mass 2916.376 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... - PLEASE NOTE You have successfully generated a topology from: 1NB1.pdb. The Amber99sb force field and the tip3p water model are used. - ETON ESAELP On the fifth line of that excerpt, I read Number of bonds was 390, now 389 and questioned what that could mean. Because of that, I wanted to verify that the topology that was successfully generated contains all the necessary bonds, so I looked through the topol.top file and saw 3 total hydrogens on the terminal nitrogen on the beginning cysteine and two total oxygens on the terminal carbon on the ending valine. Also, I did not see a bond between that nitrogen and that carbon (atoms 1 and 383); these data lead me to believe that this peptide is no longer cyclic. Construction of termini and assignment of ionization state is done with -ter. For your case, you likely need to be using -ter and selecting None. When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp -ter, I received the same message as before without any kind of interactivity for selecting options. Because of this, I tried the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp -inter -ter, which asked about the protonation of residue 24 (arginine), and when I answer none, I get this message: Processing chain 1 'A' (376 atoms, 29 residues) Which ARGININE type do you want for residue 24 0. Not protonated (charge 0) (-) 1. Protonated (charge +1) (ARG) Type a number:none --- Program
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/12/14, 4:53 PM, Matthew Stancea wrote: On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the option -ignh at the end of my command, but doing so deletes the bond between the first nitrogen and the last carbon (which should be connected for this peptide to be cyclic) and adds two additional hydrogens and a positive charge to the first nitrogen and an additional oxygen and a negative charge to the last carbon, rendering this peptide as non-cyclic. After searching around for quite a while, I found out that many others on this mailing list were having the same issues as myself, and some replies to their messages including the usage of a file known as specbond.dat which may be helpful in retaining that bond. The -ignh flag is not relevant to those observations. In my working directory, I have a file named specbond.dat and it contains the following information: 3 CYS N 1 VAL C 1 0.25CYS2VAL2 CYS SG 1 CYS SG 1 0.25CYS2CYS2 CYM SG 1 CYM SG 1 0.25CYS2CYS2 When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp while specbond.dat is in the working directory (Here is a link for the structure of peptide 1NB1 for reference if needed: http://www.ncbi.nlm.nih.gov/protein/1NB1_A ), I get the following message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYS with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- (HB3 would be the hydrogen of a cysteine residue that has not formed a disulfide bond with another amino acid residue, however my pdb does not contain an HB3). I then tried adding -ignh as per the suggestion in the twelfth line in that message. The following is a part of the message I received: Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 29 residues with 385 atoms Making bonds... Number of bonds was 390, now 389 Generating angles, dihedrals and pairs... Before cleaning: 1010 pairs Before cleaning: 1030 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 1030 dihedrals, 73 impropers, 699 angles 1007 pairs, 389 bonds and 0 virtual sites Total mass 2916.376 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... - PLEASE NOTE You have successfully generated a topology from: 1NB1.pdb. The Amber99sb force field and the tip3p water model are used. - ETON ESAELP On the fifth line of that excerpt, I read Number of bonds was 390, now 389 and questioned what that could mean. Because of that, I wanted to verify that the topology that was successfully generated contains all the necessary bonds, so I looked through the topol.top file and saw 3 total hydrogens on the terminal nitrogen on the beginning cysteine and two total oxygens on the terminal carbon on the ending valine. Also, I did not see a bond between that nitrogen and that carbon (atoms 1 and 383); these data lead me to believe that this peptide is no longer cyclic. This is related to removing duplicate bonds after merging .rtp and .tdb entries. It's normal output; there are almost always duplicates. Construction of termini and assignment of ionization state is done with -ter. For your case, you likely need to be using -ter and selecting None. When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp -ter, I received the same message as before without any kind of interactivity for selecting options. Because of this, I tried the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp -inter -ter, which asked about the protonation of residue 24 (arginine), and when I answer none, I get this message: Processing chain 1 'A' (376 atoms, 29 residues) Which ARGININE type
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the option -ignh at the end of my command, but doing so deletes the bond between the first nitrogen and the last carbon (which should be connected for this peptide to be cyclic) and adds two additional hydrogens and a positive charge to the first nitrogen and an additional oxygen and a negative charge to the last carbon, rendering this peptide as non-cyclic. After searching around for quite a while, I found out that many others on this mailing list were having the same issues as myself, and some replies to their messages including the usage of a file known as specbond.dat which may be helpful in retaining that bond. The -ignh flag is not relevant to those observations. Construction of termini and assignment of ionization state is done with -ter. For your case, you likely need to be using -ter and selecting None. However, I could not find an explanation of how to use this file in my command, and I was hoping someone could guide me on how to use specbond.dat in order to specify a particular bond. (I have tried both -chainsep specbond.dat and -merge specbond.dat.) specbond.dat is a standard file that is always read by pdb2gmx; it is not an input option. It lives in $GMXLIB but can be overridden by a copy in the local directory (as with all Gromacs library files). I have been able to make a specbond.dat file that thoroughly explains what special bonds I need pdb2gmx to account for, but when I have tried to type a command file to use it, pdb2gmx generates topology files nearly identical to the topologies of the non-cyclic peptides when I had used the -ignh option rather than generating a cyclic peptide topol.top. If more specific information is needed, I can provide that; however, I am not looking for an answer that is specific to my own issue, but rather a tutorial into generating a topology for gromacs from a pdb file of a cyclic peptide by using specbond.dat with pdb2gmx. (My version of pdb2gmx is 4.6.2.) Post the contents of your version of specbond.dat, the exact command you're issuing, and any screen output related to parsing of specbond.dat. You should only need to add one bond to the one that is provided by default. Your version of specbond.dat is either in $GMXLIB or the working directory, correct? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
