Re: [gmx-users] Heme group with CHARMM27 FF
For the benefit of anyone who happens to be Googling the same problem, the following lines inserted into the aminoacids.hdb file will tell pdb2gmx how to correctly protonate the heme. HEME16 1 1 HA CHA C1A C4D 1 1 HB CHB C4A C1B 1 1 HC CHC C4B C1C 1 1 HD CHD C4C C1D 3 4 HMA CMA C3A C4A 2 6 HAA CAA CBA C2A 2 6 HBA CBA CGA CAA 3 4 HMB CMB C2B C1B 1 1 HAB CAB C3B CBB 2 3 HBB CBB CAB C3B 3 4 HMC CMC C2C C1C 1 1 HAC CAC C3C CBC 2 3 HBC CBC CAC C3C 3 4 HMD CMD C2D C1D 2 6 HAD CAD CBD C3D 2 6 HBD CBD CGD CAD -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heme group with CHARMM27 FF
Dear Abraham, Sorry for making it hard. Since I am so new to this I guess I am not explaining it clearly for you to help me. First of all I dont want to ignore any hydrogens but as pdb2gmx was complaining about my system and suggested me to add -ignh I did so. My problem is how to update .hdb with heme hydrogen details. So, here to follow your suggestion removing the hydrogen atoms I wish to ignore I actually need to ignore the hydorgens in protein. Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 8:08 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 9:02 PM, Sundar Jubilant wrote: Dear Abraham, How would it work if I remove the hydrogen atoms that I wish to ignore from my input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for which the .hdb doesn't have information. You've never actually told us what hydrogens you want to ignore, so you're making it hard to help you. Mark In my case here, I can consider heme as a ligand instead of having it as protein since it doesn't need to be the part of the protein. Thanks for your information. Sundar -OriginalMessage- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 6:42 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 7:33 PM, Sundar Jubilant wrote: Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogen only for pretein residues but not for the heme complexed with it. No, there is no ability to ignore them selectively - but if you want to ignore any of them, you have to address the heme hydrogen database issue, or go and remove the hydrogen atoms that you wish to ignore from your input coordinate file. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. How would that really affect the accuracy of the simulation? It's not a question of accuracy, but rather that if you have bonded interactions between heme and protein, they have to be part of the same [moleculetype], which is what pdb2gmx is struggling to generate. Mark Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 3:57 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 4:38 PM, Sundar Jubilant wrote: Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a request for help, else you'll just get told to go and read), but is unlikely to get much help because you haven't identified aspecific problem. You'd like the ability tobuild hydrogen atoms on a heme residue. pdb2gmxhas to have a specific recipe for doing
Re: [gmx-users] Heme group with CHARMM27 FF
On 23/04/2012 12:01 PM, Sundar Jubilant wrote: Dear Abraham, Sorry for making it hard. Since I am so new to this I guess I am not explaining it clearly for you to help me. First of all I dont want to ignore any hydrogens but as pdb2gmx was complaining about my system and suggested me to add -ignh I did so. Since that step introduces other problems, maybe the suggestion wasn't the best approach. Identifying the real problem may lead to a better solution than trouble-shooting an issue that arose from a suggested solution. There's a lesson here about describing the whole problem when seeking help, rather than just the immediate aspect. People who might help want all the information you can give them. My problem is how to update .hdb with heme hydrogen details. So, here to follow your suggestion removing the hydrogen atoms I wish to ignore I actually need to ignore the hydorgens in protein. Maybe. Depends on the original problem. Chopping out just a subset of hydrogens with a text editor, leaving heme alone, solves a class of problems simply without needing to use the brute-force -ign and rebuild approach. Mark Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 8:08 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 9:02 PM, Sundar Jubilant wrote: Dear Abraham, How would it work if I remove the hydrogen atoms that I wish to ignore from my input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for which the .hdb doesn't have information. You've never actually told us what hydrogens you want to ignore, so you're making it hard to help you. Mark In my case here, I can consider heme as a ligand instead of having it as protein since it doesn't need to be the part of the protein. Thanks for your information. Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 6:42 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 7:33 PM, Sundar Jubilant wrote: Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogen only for pretein residues but not for the heme complexed with it. No, there is no ability to ignore them selectively - but if you want to ignore any of them, you have to address the heme hydrogen database issue, or go and remove the hydrogen atoms that you wish to ignore from your input coordinate file. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. How would that really affect the accuracy of the simulation? It's not a question of accuracy, but rather that if you have bonded interactions between heme and protein, they have to be part of the same [moleculetype], which is what pdb2gmx is struggling to generate. Mark Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 3:57 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 4:38 PM, Sundar Jubilant wrote: Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a request for help, else you'll just get told to go and read), but is unlikely to get much help because you haven't identified a specific problem. You'd like the ability to build hydrogen atoms on a heme residue. pdb2gmx has to have a specific recipe for doing that. The manual describes the required format and gives an example. Someone's going to have to do some work. I need little more detailed answer to solve the problem. By the way, here is the full command line for which I got the error. $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh If you don't ignore hydrogens, and they're already correct, you don't need to re-generate them... Mark The error is WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error
Re: [gmx-users] Heme group with CHARMM27 FF
Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. I need little more detailed answer to solve the problem. By the way, here is the full command line for which I got the error. $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh The error is WARNING: atom HA is missing in residue HEM 513 in the pdbfile You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option-missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanks. Sundar Jubilant -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 2:17 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 2:33 PM, Sundar Jubilant wrote: Dear gmx-users, I am new to Gromacs and trying to simulate a protein with a heme group using CHARMM27 ff in Gromacs 4.5.3. I havereceived the following error while running pdb2gmx . When asking for help, please give your full command lines and/or interactive selections so that we can know more context. WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option-missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can anyone help how can I generate and add hydrogen database information for heme to be used with CHARMM27 ff? You'll have to read the applicable sections of manual chapter 5, make a local copy of the charmm27.ff folder in your working directory and editing aminoacids.hdb to add the generation information. When you're done, please post your efforts so that others might be able to benefit from them in future. (Also, search first in case this has already happened!) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] Heme group with CHARMM27 FF
On 20/04/2012 4:38 PM, Sundar Jubilant wrote: Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a request for help, else you'll just get told to go and read), but is unlikely to get much help because you haven't identified a specific problem. You'd like the ability to build hydrogen atoms on a heme residue. pdb2gmx has to have a specific recipe for doing that. The manual describes the required format and gives an example. Someone's going to have to do some work. I need little more detailed answer to solve the problem. By the way, here is the full command line for which I got the error. $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh If you don't ignore hydrogens, and they're already correct, you don't need to re-generate them... Mark The error is WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanks. Sundar Jubilant -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 2:17 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 2:33 PM, Sundar Jubilant wrote: Dear gmx-users, I am new to Gromacs and trying to simulate a protein with a heme group using CHARMM27 ff in Gromacs 4.5.3. I have received the following error while running pdb2gmx . When asking for help, please give your full command lines and/or interactive selections so that we can know more context. WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can anyone help how can I generate and add hydrogen database information for heme to be used with CHARMM27 ff? You'll have to read the applicable sections of manual chapter 5, make a local copy of the charmm27.ff folder in your working directory and editing aminoacids.hdb to add the generation information. When you're done, please post your efforts so that others might be able to benefit from them in future. (Also, search first in case this has already happened!) Mark -- gmx-users mailing listgmx-us...@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it togmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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
Re: [gmx-users] Heme group with CHARMM27 FF
Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogen only for pretein residues but not for the heme complexed with it. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. How would that really affect the accuracy of the simulation? Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 3:57 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 4:38 PM, Sundar Jubilant wrote: Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a requestfor help, else you'll just get told to go and read), but is unlikelyto get much help because you haven't identified a specific problem.You'd like the ability to build hydrogen atoms on a heme residue.pdb2gmx has to have a specific recipe for doing that. The manualdescribes the required format and gives an example. Someone's goingto have to do some work. I need little more detailed answer to solve the problem. By the way, here is the full command line for which I got the error. $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh If you don't ignore hydrogens, and they're already correct, youdon't need to re-generate them... Mark The error is WARNING: atom HA is missing in residueHEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanks. Sundar Jubilant -OriginalMessage- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 2:17 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 2:33 PM, Sundar Jubilant wrote: Dear gmx-users, I am new to Gromacs and trying to simulate a protein with a heme group using CHARMM27 ff in Gromacs 4.5.3. I have received the following error while running pdb2gmx . When asking for help, please give your full command lines and/or interactive selections so that we can know more context. WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA
Re: [gmx-users] Heme group with CHARMM27 FF
On 20/04/2012 7:33 PM, Sundar Jubilant wrote: Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogen only for pretein residues but not for the heme complexed with it. No, there is no ability to ignore them selectively - but if you want to ignore any of them, you have to address the heme hydrogen database issue, or go and remove the hydrogen atoms that you wish to ignore from your input coordinate file. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. How would that really affect the accuracy of the simulation? It's not a question of accuracy, but rather that if you have bonded interactions between heme and protein, they have to be part of the same [moleculetype], which is what pdb2gmx is struggling to generate. Mark Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 3:57 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 4:38 PM, Sundar Jubilant wrote: Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a request for help, else you'll just get told to go and read), but is unlikely to get much help because you haven't identified a specific problem. You'd like the ability to build hydrogen atoms on a heme residue. pdb2gmx has to have a specific recipe for doing that. The manual describes the required format and gives an example. Someone's going to have to do some work. I need little more detailed answer to solve the problem. By the way, here is the full command line for which I got the error. $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh If you don't ignore hydrogens, and they're already correct, you don't need to re-generate them... Mark The error is WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanks. Sundar Jubilant -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 2:17 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 2:33 PM, Sundar Jubilant wrote: Dear gmx-users, I am new to Gromacs and trying to simulate a protein with a heme group using CHARMM27 ff in Gromacs 4.5.3. I have received the following error while running pdb2gmx . When asking for help, please give your full command lines and/or interactive selections so that we can know more context. WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can anyone help how can I generate and add hydrogen database information for heme to be used with CHARMM27 ff? You'll have to read the applicable sections
Re: [gmx-users] Heme group with CHARMM27 FF
Dear Abraham, How would it work if I remove the hydrogen atoms that I wish to ignore from my input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for which the .hdb doesn't have information. In my case here, I can consider heme as a ligand instead of having it as protein since it doesn't need to be the part of the protein. Thanks for your information. Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 6:42 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 7:33 PM, Sundar Jubilant wrote: Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogenonly for pretein residues but not for the heme complexedwith it. No, there is no ability to ignore them selectively - but if you wantto ignore any of them, you have to address the heme hydrogendatabase issue, or go and remove the hydrogen atoms that you wish toignore from your input coordinate file. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. Howwould that really affect the accuracy of the simulation? It's not a question of accuracy, but rather that if you have bonded interactions between heme and protein, they have to be part of thesame [moleculetype], which is what pdb2gmx is struggling togenerate. Mark Thanks Sundar -OriginalMessage- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 3:57 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 4:38 PM, Sundar Jubilant wrote: DearAbraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a request for help, else you'll just get told to go and read), but is unlikely to get much help because you haven't identified a specific problem. You'd like the ability to build hydrogen atoms on a heme residue. pdb2gmx has to have a specific recipe for doing that. The manual describes the required format and gives an example. Someone's going to have to do some work. I need little more detailed answer to solve the problem. By the way, here is the full command line for which I got the error. $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh If you don't ignore hydrogens, and they're already correct, you don't need to re-generate them... Mark The error is WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM
Re: [gmx-users] Heme group with CHARMM27 FF
On 20/04/2012 9:02 PM, Sundar Jubilant wrote: Dear Abraham, How would it work if I remove the hydrogen atoms that I wish to ignore from my input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for which the .hdb doesn't have information. You've never actually told us what hydrogens you want to ignore, so you're making it hard to help you. Mark In my case here, I can consider heme as a ligand instead of having it as protein since it doesn't need to be the part of the protein. Thanks for your information. Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 6:42 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 7:33 PM, Sundar Jubilant wrote: Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogen only for pretein residues but not for the heme complexed with it. No, there is no ability to ignore them selectively - but if you want to ignore any of them, you have to address the heme hydrogen database issue, or go and remove the hydrogen atoms that you wish to ignore from your input coordinate file. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. How would that really affect the accuracy of the simulation? It's not a question of accuracy, but rather that if you have bonded interactions between heme and protein, they have to be part of the same [moleculetype], which is what pdb2gmx is struggling to generate. Mark Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 3:57 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 4:38 PM, Sundar Jubilant wrote: Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a request for help, else you'll just get told to go and read), but is unlikely to get much help because you haven't identified a specific problem. You'd like the ability to build hydrogen atoms on a heme residue. pdb2gmx has to have a specific recipe for doing that. The manual describes the required format and gives an example. Someone's going to have to do some work. I need little more detailed answer to solve the problem. By the way, here is the full command line for which I got the error. $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh If you don't ignore hydrogens, and they're already correct, you don't need to re-generate them... Mark The error is WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanks. Sundar Jubilant -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 2:17 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 2:33 PM, Sundar Jubilant wrote: Dear gmx-users, I am new to Gromacs and trying to simulate a protein with a heme group using CHARMM27 ff in Gromacs 4.5.3. I have received the following error while running pdb2gmx . When asking for help, please give your full command lines and/or interactive selections so that we can know more context. WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb
[gmx-users] Heme group with CHARMM27 FF
Dear gmx-users, I am new to Gromacs and trying to simulate a protein with a heme group using CHARMM27 ff in Gromacs 4.5.3. I have received the following error while running pdb2gmx . WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can anyone help how can I generate and add hydrogen database information for heme to be used with CHARMM27 ff? Thanks, Sundar Jubilant -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heme group with CHARMM27 FF
On 20/04/2012 2:33 PM, Sundar Jubilant wrote: Dear gmx-users, I am new to Gromacs and trying to simulate a protein with a heme group using CHARMM27 ff in Gromacs 4.5.3. I have received the following error while running pdb2gmx . When asking for help, please give your full command lines and/or interactive selections so that we can know more context. WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There were 30 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can anyone help how can I generate and add hydrogen database information for heme to be used with CHARMM27 ff? You'll have to read the applicable sections of manual chapter 5, make a local copy of the charmm27.ff folder in your working directory and editing aminoacids.hdb to add the generation information. When you're done, please post your efforts so that others might be able to benefit from them in future. (Also, search first in case this has already happened!) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] HEME topology
Anik Sen wrote: Dear nirmal, try prodrg server for generating the topology file for the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/ PRODRG will be unable to handle this type of molecule, since it contains iron. What's more, PRODRG topologies are generally incorrect for even the simplest molecules. Several of the force fields in Gromacs contain heme parameters, otherwise they can be found in the literature. -Justin *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Nirmal Prasad [nimmynir...@gmail.com] *Sent:* Wednesday, January 11, 2012 9:45 AM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] HEME topology Hello, Can any one send topology for Heme group..My work is stuckeup here are the PDB parameters for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00 HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00 HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00 HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00 HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00 HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00 HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00 HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00 HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00 HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00 HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00 HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00 HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00 HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00 HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00 HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00 HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00 HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00 HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00 HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00 HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00 HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00 HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00 HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00 HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00 HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00 HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00 HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00 HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00 HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00 HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00 HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00 HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00 HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00 HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00 HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00 HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00 HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00 HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00 HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00 HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00 HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00 TER3894 HEM 482 thanks in advance nirmal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] HEME topology
Hello, Can any one send topology for Heme group..My work is stuckeup here are the PDB parameters for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00 HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00 HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00 HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00 HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00 HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00 HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00 HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00 HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00 HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00 HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00 HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00 HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00 HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00 HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00 HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00 HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00 HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00 HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00 HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00 HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00 HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00 HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00 HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00 HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00 HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00 HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00 HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00 HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00 HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00 HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00 HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00 HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00 HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00 HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00 HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00 HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00 HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00 HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00 HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00 HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00 HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00 TER3894 HEM 482 thanks in advance nirmal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] HEME topology
Dear nirmal, try prodrg server for generating the topology file for the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Nirmal Prasad [nimmynir...@gmail.com] Sent: Wednesday, January 11, 2012 9:45 AM To: Discussion list for GROMACS users Subject: [gmx-users] HEME topology Hello, Can any one send topology for Heme group..My work is stuckeup here are the PDB parameters for HEME --- HETATM 3851 FE HEM 482 4.876 25.216 23.893 1.00 0.00 HETATM 3852 CHA HEM 482 5.264 25.759 20.480 1.00 0.00 HETATM 3853 CHB HEM 482 8.132 24.660 24.172 1.00 0.00 HETATM 3854 CHC HEM 482 4.480 24.399 27.195 1.00 0.00 HETATM 3855 CHD HEM 482 1.700 25.148 23.458 1.00 0.00 HETATM 3856 NA HEM 482 6.466 25.218 22.555 1.00 0.00 HETATM 3857 C1A HEM 482 6.439 25.484 21.193 1.00 0.00 HETATM 3858 C2A HEM 482 7.778 25.464 20.681 1.00 0.00 HETATM 3859 C3A HEM 482 8.610 25.197 21.767 1.00 0.00 HETATM 3860 C4A HEM 482 7.741 25.081 22.906 1.00 0.00 HETATM 3861 CMA HEM 482 10.215 25.091 21.758 1.00 0.00 HETATM 3862 CAA HEM 482 8.230 25.628 19.242 1.00 0.00 HETATM 3863 CBA HEM 482 8.574 27.061 18.804 1.00 0.00 HETATM 3864 CGA HEM 482 9.117 27.044 17.359 1.00 0.00 HETATM 3865 O1A HEM 482 9.982 27.831 17.013 1.00 0.00 HETATM 3866 O2A HEM 482 8.739 26.229 16.541 1.00 0.00 HETATM 3867 NB HEM 482 6.104 24.497 25.449 1.00 0.00 HETATM 3868 C1B HEM 482 7.444 24.359 25.345 1.00 0.00 HETATM 3869 C2B HEM 482 8.044 24.034 26.598 1.00 0.00 HETATM 3870 C3B HEM 482 6.961 23.930 27.496 1.00 0.00 HETATM 3871 C4B HEM 482 5.778 24.182 26.693 1.00 0.00 HETATM 3872 CMB HEM 482 9.563 23.973 26.877 1.00 0.00 HETATM 3873 CAB HEM 482 6.964 23.552 28.851 1.00 0.00 HETATM 3874 CBB HEM 482 8.069 23.513 29.865 1.00 0.00 HETATM 3875 NC HEM 482 3.315 24.748 25.179 1.00 0.00 HETATM 3876 C1C HEM 482 3.331 24.678 26.492 1.00 0.00 HETATM 3877 C2C HEM 482 2.053 24.644 27.006 1.00 0.00 HETATM 3878 C3C HEM 482 1.187 24.668 25.881 1.00 0.00 HETATM 3879 C4C HEM 482 2.053 24.742 24.763 1.00 0.00 HETATM 3880 CMC HEM 482 1.716 24.541 28.529 1.00 0.00 HETATM 3881 CAC HEM 482 -0.191 24.700 25.725 1.00 0.00 HETATM 3882 CBC HEM 482 -1.163 24.945 26.680 1.00 0.00 HETATM 3883 ND HEM 482 3.655 25.286 22.181 1.00 0.00 HETATM 3884 C1D HEM 482 2.373 25.199 22.282 1.00 0.00 HETATM 3885 C2D HEM 482 1.768 25.396 21.008 1.00 0.00 HETATM 3886 C3D HEM 482 2.780 25.600 20.124 1.00 0.00 HETATM 3887 C4D HEM 482 3.958 25.545 20.924 1.00 0.00 HETATM 3888 CMD HEM 482 0.252 25.372 20.693 1.00 0.00 HETATM 3889 CAD HEM 482 2.755 25.897 18.597 1.00 0.00 HETATM 3890 CBD HEM 482 2.710 27.455 18.272 1.00 0.00 HETATM 3891 CGD HEM 482 2.759 27.846 16.738 1.00 0.00 HETATM 3892 O1D HEM 482 2.411 29.018 16.323 1.00 0.00 HETATM 3893 O2D HEM 482 3.210 26.948 15.911 1.00 0.00 TER3894 HEM 482 thanks in advance nirmal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Heme group in the forcefield gromos53a6
Dear users, We are trying to perform a MD simulation of a protein with a heme group using the gromos53a6 force field but when trying to run grompp we receive the error mesage: Program grompp, VERSION 4.0.3 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype FE2+ not found How can it happen if the gromos53a6 force field have parameters to the heme group ? Does someone knows how to fix it ? Tanos Celmar Costa Franca - D.Sc Coordenador do Programa de Pos-graduacão em Química Secão de Engenharia Química - SE/5 Instituto Militar de Engenharia - IME Rio de Janeiro - RJ Brasil This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Heme group in the forcefield gromos53a6
Tanos Celmar Costa Franca wrote: Dear users, We are trying to perform a MD simulation of a protein with a heme group using the gromos53a6 force field but when trying to run grompp we receive the error mesage: Program grompp, VERSION 4.0.3 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype FE2+ not found How can it happen if the gromos53a6 force field have parameters to the heme group ? Does someone knows how to fix it ? Heme parameters are included in 53A6, but they don't make reference to any such FE2+ atomtype. The .rtp and .atp files specify an FE atomtype, though. You're still probably going to run into missing bonded parameters for the connection between your protein and heme. I don't know what the solution for that is, though. Also, unless you have a specific reason for using a Gromacs version that is two years old (as of today, exactly!) then you should upgrade to a more recent (preferably the most recent) version, to take advantage of numerous bug fixes and feature additions. http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.0.x -Justin Tanos Celmar Costa Franca - D.Sc Coordenador do Programa de Pos-graduacão em Química Secão de Engenharia Química - SE/5 Instituto Militar de Engenharia - IME Rio de Janeiro - RJ Brasil This message was sent using IMP, the Internet Messaging Program. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] heme
Hi Erik I am using ffG43a1 force field. It has heme topology. But in Cyt C. FE is bonded to both NR of HIS and SD of MET. The parameter for the bond, FE SD, angles e.g. NR (HIS) FE SD(MET) and dihedral angle CH2(MET) SD (MET) FE NR(HIS) is missing in this force field. hence I am getting error while running grompp. Please suggest me what should I do. Shahid Nayeem On Thu, Nov 25, 2010 at 3:12 AM, Erik Marklund er...@xray.bmc.uu.se wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] heme
Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] heme
shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] heme
Erik Marklund wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? The same problem is frequently reported. The inter-residue bonds and angles are not assigned in pdb2gmx, nor are they present in the force field, IIRC. Hence the fatal errors. Perhaps something has changed since a long time ago, but I am sure problems exist in recent versions. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] heme
I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but Met SD and FE bond is not there. Shahid Nayeem On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul jalem...@vt.edu wrote: Erik Marklund wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem A long time ago I simulated CytC with one of the gromos force fields. It worked right out of the box. What forcefield are you using? The same problem is frequently reported. The inter-residue bonds and angles are not assigned in pdb2gmx, nor are they present in the force field, IIRC. Hence the fatal errors. Perhaps something has changed since a long time ago, but I am sure problems exist in recent versions. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] HEME-cysteine gromacs simulation
HI all: I want to run a simulation with heme group(cytochrome p450). i have made a 3-d structure model for a cytochrome p450 .I use the ffG43a1 force field,someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots of papers,but most of them used amber force field.Befor runing the gromacs molecular simulation,i define the heme group as a new residue in the .rtp files,following the required formats(atoms,bonds exclusions,angles,impropers,dihedrals)and then define a new FE-S bong. i run the simulation like this: pdb2gmx -ignh -ff G43a1 -f CYP2W1_CYSHEME.pdb -o new1.pdb -p new1.top -water spce editconf -bt cubic -f new1.pdb -o new2.pdb -d 0.9 genbox -cp new2.pdb -cs spc216.gro -o new3.pdb -p new1.top grompp -f em.mdp -c new3.pdb -p new1.top -o em.tpr genion -s em.tpr -o new5.pdb -nname CL- -nn 1 -g ion.log; Edit top file, delette em.tpr grompp -f em.mdp -c new5.pdb -p new1.top -o em.tpr mdrun -s em.tpr -o em.trr -c new7.pdb -g em.log -e em.edr grompp -f pr.mdp -c new7.pdb -p new1.top -o pr.tpr mdrun -s pr.tpr -o pr.trr -c new9.mdp -e pr.edr -g pr.log 1 i run pdb2gmx and get the new1.pdb ,when checking the pdb with accelrys ds visualizer or sybyl,the atom FE was recognized as F (Fluorine)and the pdb miss the bonds between FE-S FE-N,i add or delete a blank space befor or after the FE in the pdb file,it was read as iron(FE) again but still missing;when checking the .top file,there was a FE (both atom name and type)and formed the FE-S FE-N bonds. if i ignore the above things,go on the command ,when runing the em.mdp there is a tip that Steepest Descents failed converged to Fmax 1000 in 5001 steps.when run the pr.tpr,a error emerged as segment fatal error。 2 someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots of papers,but most of them used amber force field.Does anyone known a paper with a gromacs force field for HEME group? please help me how handle those problems,how can i go on the simulation? the HEME-cysteine parameter in the rtp files,define themas a new residue.(is there any problems?) [ HEME ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2-0.1 2 SG S-0.4 2 C C 0.38000 3 O O-0.38000 3 FEFE 0.84700 4 NANR-0.37000 4 NBNR-0.42300 4 NCNR-0.50400 4 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBSGgb_30 SGFEgb_48 FENAgb_34 FENBgb_34 FENCgb_34 FENDgb_34 . [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 ... [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 FESGNAND gi_3 FESGNANB gi_3 FESGNBNC gi_3 FESGNCND gi_3 . [ dihedrals ] ; aiajakal gromos type . 没有广告的终身免费邮箱,www.yeah.net 没有广告的终身免费邮箱,www.yeah.net___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] HEME-cysteine gromacs simulation
?? wrote: HI all: I want to run a simulation with heme group(cytochrome p450). i have made a 3-d structure model for a cytochrome p450 .I use the ffG43a1 force field,someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots of papers,but most of them used amber force field.Befor runing the gromacs molecular simulation,i define the heme group as a new residue in the .rtp files,following the required formats(atoms,bonds exclusions,angles,impropers,dihedrals)and then define a new FE-S bong. i run the simulation like this: pdb2gmx -ignh -ff G43a1 -f CYP2W1_CYSHEME.pdb -o new1.pdb -p new1.top -water spce editconf -bt cubic -f new1.pdb -o new2.pdb -d 0.9 genbox -cp new2.pdb -cs spc216.gro -o new3.pdb -p new1.top grompp -f em.mdp -c new3.pdb -p new1.top -o em.tpr genion -s em.tpr -o new5.pdb -nname CL- -nn 1 -g ion.log; Edit top file, delette em.tpr grompp -f em.mdp -c new5.pdb -p new1.top -o em.tpr mdrun -s em.tpr -o em.trr -c new7.pdb -g em.log -e em.edr grompp -f pr.mdp -c new7.pdb -p new1.top -o pr.tpr mdrun -s pr.tpr -o pr.trr -c new9.mdp -e pr.edr -g pr.log 1 i run pdb2gmx and get the new1.pdb ,when checking the pdb with accelrys ds visualizer or sybyl,the atom FE was recognized as F (Fluorine)and the pdb miss the bonds between FE-S FE-N,i add or delete a blank space befor or after the FE in the pdb file,it was read as iron(FE) again but still missing;when checking the .top file,there was a FE (both atom name and type)and formed the FE-S FE-N bonds. Visualization programs have to use heuristics to guess where bonds are and what names occur for which atoms (HG1 might be mercury or the first hydrogen on a gamma carbon, NE might be neon or an epsilon nitrogen, etc.). Only if you are able to read in a .tpr (such as with ngmx distributed inside GROMACS) can you get any visual confirmation of what GROMACS thinks you have described in your topology. There is no standardized widely-used mechanism for including such information in a PDB file, and so such usage of a file is unreliable. if i ignore the above things,go on the command ,when runing the em.mdp there is a tip that Steepest Descents failed converged to Fmax 1000 in 5001 steps.when run the pr.tpr,a error emerged as segment fatal error?? Read the .log files as well. GROMACS almost never segfaults (except when subjected to buggy MPI libraries), and when it does it will normally write some diagnostic information to stdout or the .log file. 2 someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots of papers,but most of them used amber force field.Does anyone known a paper with a gromacs force field for HEME group? Sorry, I can't help there. please help me how handle those problems,how can i go on the simulation? the HEME-cysteine parameter in the rtp files,define themas a new residue.(is there any problems?) Look at the results in ngmx to get started. Try generating a structure for some minimalist version of the heme group and get EM and MD to work on that first. If you reduce the complexity, you can eliminate potential sources of problems until you find the source. Mark [ HEME ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2-0.1 2 SG S-0.4 2 C C 0.38000 3 O O-0.38000 3 FEFE 0.84700 4 NANR-0.37000 4 NBNR-0.42300 4 NCNR-0.50400 4 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBSGgb_30 SGFEgb_48 FENAgb_34 FENBgb_34 FENCgb_34 FENDgb_34 . [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 ... [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N
[gmx-users] HEME-cysteine gromacs simulation
You always need a correct topology. The main issue here is that you need to have correct parameters. Where did you get your heme and Fe parameters? Were you careful about the Fe state oxidation state? I suspect that most people use Amber because of their antechamber program, which seems like a brilliant idea even if it may overstretch it's own parameterization without letting you know. I have no specific advice for you here beyond saying that it is worth spending a month figuring out what parameters you should really be using (hint: why would you be using ffG43a1 if most others use Amber here? do you know something that they don't?). This will end up saving you time in the long run. Note that ffG43a1 is the GROMOS forcefield, not the GROMACS forcefield. It is unfortunate that many programs (Amber, Charmm, gromacs) have their own similarly named forcefield, but that does not mean that the forcefield must be used with the associated program. There are forcefields that are not associated with a program (OPLS) and programs that never developed their own force field (NAMD, Desmond, Tinker, LAMMPS), so it is perfectly ok for you to use the amber forcefield with the gromacs program. Bottom line: read, read, read. Chris. -- original message -- I want to run a simulation with heme group(cytochrome p450). i have made a 3-d structure model for a cytochrome p450 .I use the ffG43a1 force field,someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots of papers,but most of them used amber force field.Befor runing the gromacs molecular simulation,i define the heme group as a new residue in the .rtp files,following the required formats(atoms,bonds exclusions,angles,impropers,dihedrals)and then define a new FE-S bong. i run the simulation like this: pdb2gmx -ignh -ff G43a1 -f CYP2W1_CYSHEME.pdb -o new1.pdb -p new1.top -water spce editconf -bt cubic -f new1.pdb -o new2.pdb -d 0.9 genbox -cp new2.pdb -cs spc216.gro -o new3.pdb -p new1.top grompp -f em.mdp -c new3.pdb -p new1.top -o em.tpr genion -s em.tpr -o new5.pdb -nname CL- -nn 1 -g ion.log; Edit top file, delette em.tpr grompp -f em.mdp -c new5.pdb -p new1.top -o em.tpr mdrun -s em.tpr -o em.trr -c new7.pdb -g em.log -e em.edr grompp -f pr.mdp -c new7.pdb -p new1.top -o pr.tpr mdrun -s pr.tpr -o pr.trr -c new9.mdp -e pr.edr -g pr.log 1 i run pdb2gmx and get the new1.pdb ,when checking the pdb with accelrys ds visualizer or sybyl,the atom FE was recognized as F (Fluorine)and the pdb miss the bonds between FE-S FE-N,i add or delete a blank space befor or after the FE in the pdb file,it was read as iron(FE) again but still missing;when checking the .top file,there was a FE (both atom name and type)and formed the FE-S FE-N bonds. if i ignore the above things,go on the command ,when runing the em.mdp there is a tip that Steepest Descents failed converged to Fmax 1000 in 5001 steps.when run the pr.tpr,a error emerged as segment fatal error¡£ 2 someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots of papers,but most of them used amber force field.Does anyone known a paper with a gromacs force field for HEME group? please help me how handle those problems,how can i go on the simulation? the HEME-cysteine parameter in the rtp files,define themas a new residue.(is there any problems?) [ HEME ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2-0.1 2 SG S-0.4 2 C C 0.38000 3 O O-0.38000 3 FEFE 0.84700 4 NANR-0.37000 4 NBNR-0.42300 4 NCNR-0.50400 4 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBSGgb_30 SGFEgb_48 FENAgb_34 FENBgb_34 FENCgb_34 FENDgb_34 . [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 ... [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 FESGNAND gi_3 FESGNANB gi_3 FESGNBNC gi_3 FESGNCND gi_3 . [ dihedrals ] ; aiajakal gromos type . ûÓйã¸æµÄÖÕÉíÃâ·ÑÓÊÏä,www.yeah.net ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search
Re: [gmx-users] HEME topology
Also is there some heme topology in the public domain that I can compare my parametrisation with ? at the amber parameter database, all and united atom. http://www.pharmacy.manchester.ac.uk/bryce/amber tim ___ 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] HEME topology
Hi, I am trying to simulate HEME in a water box. I generated HEME topology based on the parameters in the ffG43a2.rtp file. When I run a short burst of unrestrained dynamics, it does not remain planar. I understand that there might be some buckling but not to the extent that I am observing. My questions is - Do I need to add some more parameters other than the default ones in the .top file ? (Impropers and Dihedrals already exist with planar flags) Also is there some heme topology in the public domain that I can compare my parametrisation with ? Many thanks Shozeb Haider The London School of Pharmacy ___ 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] HEME topology
Take a look at the charm file: top_all22_prot.inp Specifically, RESI HEME ___ 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] Heme-O2 parameters
Dear All, I'm looking for gromacs parameters for heme bound to oxygen molecule . I will appreciate getting the parameters or any tip considering the best way to create them. Thank you Rotem Sertchook ___ 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] Heme-O2 parameters
If they are not among the user contributions, and if they are not published somewhere in the literature, you will have to derive them yourself (an advanced topic!). See here: http://wiki.gromacs.org/index.php/Parameterization And this one is probably applicable in your case, as well: http://wiki.gromacs.org/index.php/Exotic_Species -Justin Rotem Sertchook wrote: Dear All, I'm looking for gromacs parameters for heme bound to oxygen molecule . I will appreciate getting the parameters or any tip considering the best way to create them. Thank you Rotem Sertchook ___ 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 thewww 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 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] HEME simulation
Dear all, I am trying to run a simulation of the interaction between two HEME in water. I have done it without problem, but when I use the calculated charge of HEME atoms from ab initio calculation I have problem. The enery minimaization was run without problem with the results: Steepest Descents converged to Fmax 2000 in 84 steps Potential Energy = -1.5738966e+05 Maximum force = 1.8819653e+03 on atom 77 Norm of force = 9.0745400e+03 When I try to run position restraint dynamic the process end with error as follow: t = 1.108 ps: Water molecule starting at atom 10423 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates. I checked the simulation and I see some of atoms are transfered to the out of the box. I reduced timestep and changed box type and coulombtype and deleted some water, but I didn t have any result. Also, the charge in my topology file is as follow: FE1.31 NA -0.78 NB -0.81 NC -0.8 ND -0.79 CHA0.33 HHA0.0 C1A0.24 C2A0.04 C3A0.06 C4A0.22 CMA0.03 CAA0.02 CBA0.07 CGA0.5 O1A-0.18 O2A-0.46 CHB0.04 HHB0.0 C1B0.22 C2B0.06 C3B-0.02 C4B0.22 CMB0.03 CAB0.07 CBB-0.01 CHC0.05 HHC0.0 C1C0.22 C2C0.06 C3C-0.03 C4C0.22 CMC0.02 CAC0.08 CBC-0.01 CHD0.05 HHD0.0 C1D0.23 C2D0.05 C3D0.04 C4D0.24 CMD0.03 CAD0.0 CBD0.0 CGD0.41 O1D-0.61 O2D-0.66 H1A0.0 What should I do? Thanks a lot Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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] HEME simulation
gromacs user wrote: Dear all, I am trying to run a simulation of the interaction between two HEME in water. I have done it without problem, but when I use the calculated charge of HEME atoms from ab initio calculation I have problem. The enery minimaization was run without problem with the results: Steepest Descents converged to Fmax 2000 in 84 steps Potential Energy = -1.5738966e+05 Maximum force = 1.8819653e+03 on atom 77 Norm of force = 9.0745400e+03 When I try to run position restraint dynamic the process end with error as follow: check your energy components. are the bonds and angles low enough (this is in the minimization). How do the values differ in the dynamics? -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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
