Re: [gmx-users] force field / parameters for NADH, FMN
Hi Justin, just for testing, I applied cgenff_charmm2gmx.py with charmm36-nov2016.ff as it has the same CGenFF version: --Version of CGenFF detected in /usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/forcefield.doc : 3.0.1 But I still get the same warnings and errors. Would you still recommend me to use the existing parameters and delete the respective lines from the str file? Thank you in advance! All the best Johannes On 05.11.2017 18:12, Justin Lemkul wrote: On 11/3/17 10:33 AM, Hermann, Johannes wrote: Hey Justin, thanks - again - for your reply! Now I get duplicated parameters warnings and errors: WARNING 1 [file fmn.prm, line 5]: Overriding Bond parameters. old: 0.1295 405848 0.1295 405848 new: CG2R64 NG2D1 1 0.1414 255224.00 [...] ERROR 1 [file fmn.prm, line 35]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. [...] I did *not* tick the "Include parameters that are already in CGenFF" on the webserver when generating the str file. I am using the newest version of cgenff_charmm2gmx.py. Do you have any hint for me? Well, you've managed to stumble across a case where the version difference *does* actually matter. Use whatever the existing parameters are for the conflicting types, not the ones in your .str file. Your parameters assume the interactions are unknown and is making a guess at them; the ones in the CGenFF 4.0 parameter set have been specifically optimized. -Justin -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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] force field / parameters for NADH, FMN
On 11/3/17 10:33 AM, Hermann, Johannes wrote: Hey Justin, thanks - again - for your reply! Now I get duplicated parameters warnings and errors: WARNING 1 [file fmn.prm, line 5]: Overriding Bond parameters. old: 0.1295 405848 0.1295 405848 new: CG2R64 NG2D1 1 0.1414 255224.00 [...] ERROR 1 [file fmn.prm, line 35]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. [...] I did *not* tick the "Include parameters that are already in CGenFF" on the webserver when generating the str file. I am using the newest version of cgenff_charmm2gmx.py. Do you have any hint for me? Well, you've managed to stumble across a case where the version difference *does* actually matter. Use whatever the existing parameters are for the conflicting types, not the ones in your .str file. Your parameters assume the interactions are unknown and is making a guess at them; the ones in the CGenFF 4.0 parameter set have been specifically optimized. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] force field / parameters for NADH, FMN
Hey Justin, thanks - again - for your reply! Now I get duplicated parameters warnings and errors: WARNING 1 [file fmn.prm, line 5]: Overriding Bond parameters. old: 0.1295 405848 0.1295 405848 new: CG2R64 NG2D1 1 0.1414 255224.00 [...] ERROR 1 [file fmn.prm, line 35]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. [...] I did *not* tick the "Include parameters that are already in CGenFF" on the webserver when generating the str file. I am using the newest version of cgenff_charmm2gmx.py. Do you have any hint for me? Thanks in advance! All the best Johannes On 03.11.2017 13:18, Justin Lemkul wrote: On 11/3/17 8:17 AM, Hermann, Johannes wrote: Dear Justin, thanks for the hint with the CHARMM-formatted topology and parameter files! That is great help! I had a different atom number compared to NAI and NADH because I had a different (non-physical) protonation state. The text drawing helped me a lot to figure out the few Nomenclature differences between my pdb and the NAI in rtp file. For my other coenzyme, Flavin mononucleotide (FMN), I got the mol2 file from the ZINC Database and applied cgenff.paramchem.org and converted it with your python script (cgenff_charmm2gmx.py) to Gromacs format. I now have the following issue: The CGenFF version on the webserver is 3.0.1 NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in fmn.str : 3.0.1 Therefore, I should use the charmm36-nov2016 ff: --Version of CGenFF detected in charmm36-nov2016.ff/forcefield.doc : 3.0.1 BUT: NAI is only present in charmm36-jul2017 ff, which uses CGenFF version 4.0 --Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 4.0 Do you have any suggestion on how I could resolve this issue? Ignore it. The differences between the two are not relevant here. It has taken an unfortunately long time to get the CGenFF server updated and I don't know when it will happen. -Justin -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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] force field / parameters for NADH, FMN
On 11/3/17 8:17 AM, Hermann, Johannes wrote: Dear Justin, thanks for the hint with the CHARMM-formatted topology and parameter files! That is great help! I had a different atom number compared to NAI and NADH because I had a different (non-physical) protonation state. The text drawing helped me a lot to figure out the few Nomenclature differences between my pdb and the NAI in rtp file. For my other coenzyme, Flavin mononucleotide (FMN), I got the mol2 file from the ZINC Database and applied cgenff.paramchem.org and converted it with your python script (cgenff_charmm2gmx.py) to Gromacs format. I now have the following issue: The CGenFF version on the webserver is 3.0.1 NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in fmn.str : 3.0.1 Therefore, I should use the charmm36-nov2016 ff: --Version of CGenFF detected in charmm36-nov2016.ff/forcefield.doc : 3.0.1 BUT: NAI is only present in charmm36-jul2017 ff, which uses CGenFF version 4.0 --Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 4.0 Do you have any suggestion on how I could resolve this issue? Ignore it. The differences between the two are not relevant here. It has taken an unfortunately long time to get the CGenFF server updated and I don't know when it will happen. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] force field / parameters for NADH, FMN
Dear Justin, thanks for the hint with the CHARMM-formatted topology and parameter files! That is great help! I had a different atom number compared to NAI and NADH because I had a different (non-physical) protonation state. The text drawing helped me a lot to figure out the few Nomenclature differences between my pdb and the NAI in rtp file. For my other coenzyme, Flavin mononucleotide (FMN), I got the mol2 file from the ZINC Database and applied cgenff.paramchem.org and converted it with your python script (cgenff_charmm2gmx.py) to Gromacs format. I now have the following issue: The CGenFF version on the webserver is 3.0.1 NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in fmn.str : 3.0.1 Therefore, I should use the charmm36-nov2016 ff: --Version of CGenFF detected in charmm36-nov2016.ff/forcefield.doc : 3.0.1 BUT: NAI is only present in charmm36-jul2017 ff, which uses CGenFF version 4.0 --Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 4.0 Do you have any suggestion on how I could resolve this issue? Thank you very much in advance! All the best Johannes On 02.11.2017 17:12, Justin Lemkul wrote: On 11/2/17 12:05 PM, Hermann, Johannes wrote: Dear Justin, dear all, thank you for your reply. I will test the web server when I have managed to generate the mol2 file for FMN. I had a look in the rtp file of charmm36 ff and I detected that there are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code for the reduced form of NAD+ (https://www4.rcsb.org/ligand/NAI), i.e. NADH. However, both NAI and NADH in the rtp file have only 71 atoms, while they should have 73. Hence, if I am not mistaken, NAI and NADH are both NAD (not NADH or NAD+). Has anyone who is reading this a ff field which he can send me? This would save me a lot of time. Anyone using the CHARMM force field should go to the MacKerell website and download the CHARMM-formatted topology and parameter files - they contain full chemical names and text drawings of structures. Unfortunately, there is no easy way to port all of this stuff to GROMACS so it gets lost. But if you ever need clarification, go to the source. NAD1: oxidized NAD (so it is NAD+), net charge -1 NAI and NADH: reduced NAD (so it is NADH), net charge -2 I don't know the history of why there are both NAI and NADH residues. -Justin -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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] force field / parameters for NADH, FMN
On 11/2/17 12:05 PM, Hermann, Johannes wrote: Dear Justin, dear all, thank you for your reply. I will test the web server when I have managed to generate the mol2 file for FMN. I had a look in the rtp file of charmm36 ff and I detected that there are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code for the reduced form of NAD+ (https://www4.rcsb.org/ligand/NAI), i.e. NADH. However, both NAI and NADH in the rtp file have only 71 atoms, while they should have 73. Hence, if I am not mistaken, NAI and NADH are both NAD (not NADH or NAD+). Has anyone who is reading this a ff field which he can send me? This would save me a lot of time. Anyone using the CHARMM force field should go to the MacKerell website and download the CHARMM-formatted topology and parameter files - they contain full chemical names and text drawings of structures. Unfortunately, there is no easy way to port all of this stuff to GROMACS so it gets lost. But if you ever need clarification, go to the source. NAD1: oxidized NAD (so it is NAD+), net charge -1 NAI and NADH: reduced NAD (so it is NADH), net charge -2 I don't know the history of why there are both NAI and NADH residues. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] force field / parameters for NADH, FMN
Dear Justin, dear all, thank you for your reply. I will test the web server when I have managed to generate the mol2 file for FMN. I had a look in the rtp file of charmm36 ff and I detected that there are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code for the reduced form of NAD+ (https://www4.rcsb.org/ligand/NAI), i.e. NADH. However, both NAI and NADH in the rtp file have only 71 atoms, while they should have 73. Hence, if I am not mistaken, NAI and NADH are both NAD (not NADH or NAD+). Has anyone who is reading this a ff field which he can send me? This would save me a lot of time. Thanks in advance! All the best Johannes On 30.10.2017 16:14, Justin Lemkul wrote: On 10/30/17 10:58 AM, Hermann, Johannes wrote: Dear all, I want to simulate a complex consisting of a protein, FMN, and NADH. I have two problems/questions: 1) In the "CHARMM36 all-atom force field (March 2017)" parameters for NADH are present. But apparently I am using a wrong atom naming convention (I copied / pasted NADH from a pdb entry): Fatal error: Atom PN in residue NADH 0 was not found in rtp entry NADH with 71 atoms while sorting atoms. How can I generate a appropriate input file for gromacs gmx2pdb? Make the PDB file atom names match those of the .rtp entry. It's a bit awkward but everyone seems to have a different convention for naming cofactor atoms. 2) I did not find FMN in the charmm36 force field. Can some recommend me a program to generate a parameter file? And how to proceed with it? If it's not in CHARMM, use CGenFF. There's a web server that will parametrize it (cgenff.paramchem.org) and tell you how good the topology is so you can decide if you need to do any manual parametrization. Download the .str -> .itp conversion script from the MacKerell lab webpage and you're ready for GROMACS. -Justin -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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] force field / parameters for NADH, FMN
On 10/30/17 10:58 AM, Hermann, Johannes wrote: Dear all, I want to simulate a complex consisting of a protein, FMN, and NADH. I have two problems/questions: 1) In the "CHARMM36 all-atom force field (March 2017)" parameters for NADH are present. But apparently I am using a wrong atom naming convention (I copied / pasted NADH from a pdb entry): Fatal error: Atom PN in residue NADH 0 was not found in rtp entry NADH with 71 atoms while sorting atoms. How can I generate a appropriate input file for gromacs gmx2pdb? Make the PDB file atom names match those of the .rtp entry. It's a bit awkward but everyone seems to have a different convention for naming cofactor atoms. 2) I did not find FMN in the charmm36 force field. Can some recommend me a program to generate a parameter file? And how to proceed with it? If it's not in CHARMM, use CGenFF. There's a web server that will parametrize it (cgenff.paramchem.org) and tell you how good the topology is so you can decide if you need to do any manual parametrization. Download the .str -> .itp conversion script from the MacKerell lab webpage and you're ready for GROMACS. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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.
[gmx-users] force field / parameters for NADH, FMN
Dear all, I want to simulate a complex consisting of a protein, FMN, and NADH. I have two problems/questions: 1) In the "CHARMM36 all-atom force field (March 2017)" parameters for NADH are present. But apparently I am using a wrong atom naming convention (I copied / pasted NADH from a pdb entry): Fatal error: Atom PN in residue NADH 0 was not found in rtp entry NADH with 71 atoms while sorting atoms. How can I generate a appropriate input file for gromacs gmx2pdb? 2) I did not find FMN in the charmm36 force field. Can some recommend me a program to generate a parameter file? And how to proceed with it? Thank you all in advance! All the best Johannes -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.de/ -- 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.
