Re: [gmx-users] charm in gromacs
On 18/05/2012 8:02 PM, francesco oteri wrote: Hi, at the link http://dl.dropbox.com/u/40545409/charmm2itp.tgz you can find the files I am using Files ffcharmmnb.itp ffcharmmbon.itp have been generated through: convert_charmm_to_gromacs.pl http://convert_charmm_to_gromacs.pl/ par_all36_carb.prm while carbohydrates.rtp and carbohydrates.rtp through a script of mine. Now, if you look at [ dihedraltypes ] section in file ffcharmmbon.itp, there are strange things: 1) dihedrals defined once, are converted Ryckaert-Bellemans form, while the armonic form should be more clear. Anyway, it just a matter of style so I dont complan about. 2) dihedrals with multiple definitions ( OC30P CC3162 CC3161 OC311 at line 598 in file ffcharmmbon.itp, for example) are defined as: OC30P CC3162 CC3161 OC311 3 20.92 41.84 16.74 -41.84 0 0 ; 30P CC3162 CC3161 OC311 1 180 10.46 1 ; 30P CC3162 CC3161 OC311 1 0 8.368 2 ; 30P CC3162 CC3161 OC311 1 0 10.46 3 The commented lines clearly display the multiple definition, that can be described using function 9 ... which didn't exist at the time of my writing of that script, as the comments in the script discuss. Hence solution 1), which was adequate for the subset of CHARMM27 that was of interest to me. 3) An other problem rise with impropers dihedrals. Any of them are defined as Ryckaert-Bellemans, ex. HCA1 CC3161 CC3162 OC311 3 0.5858 1.757 0 -2.343 0 0 at line 926 of ffcharmmbon.itp while points 1 and 2 don't impact on the correctness of the simulation and can be bypassed defining [ bondedtypes ] section as following 1 5 321 3 1 0 Problem 3 cannot be solved without manipulating the ffcharmmbon.itp. In fact, since some impropers are defined as functiontype 2 other as functiontype 3, so there is not an unique bondedtypes definition covering both the definition. Did I any mistake or actually there is a problem in the script? IIRC CHARMM36 is more recent than that script, so the assumptions made by the script for CHARMM27 may not be applicable. If CHARMM36 uses more than one kind of improper dihedral, then I would not expect the script to function correctly in this regard. You would need to modify the script or its output. Mark Francesco 2012/5/18 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 18/05/2012 2:52 AM, francesco oteri wrote: Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl http://convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion This assumption is no longer valid, is it? As far as I know, infact, now gromacs support multiple periodic function (funtion 9), is it? Correct, but with the inclusion of native CHARMM27 in GROMACS, I have had no reason to upgrade these conversion scripts to support function type 9. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- 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] charm in gromacs
On 18/05/2012 2:52 AM, francesco oteri wrote: Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl http://convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion This assumption is no longer valid, is it? As far as I know, infact, now gromacs support multiple periodic function (funtion 9), is it? Correct, but with the inclusion of native CHARMM27 in GROMACS, I have had no reason to upgrade these conversion scripts to support function type 9. 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] charm in gromacs
Hi, at the link http://dl.dropbox.com/u/40545409/charmm2itp.tgz you can find the files I am using Files ffcharmmnb.itp ffcharmmbon.itp have been generated through: convert_charmm_to_gromacs.pl par_all36_carb.prm while carbohydrates.rtp and carbohydrates.rtp through a script of mine. Now, if you look at [ dihedraltypes ] section in file ffcharmmbon.itp, there are strange things: 1) dihedrals defined once, are converted Ryckaert-Bellemans form, while the armonic form should be more clear. Anyway, it just a matter of style so I dont complan about. 2) dihedrals with multiple definitions ( OC30P CC3162 CC3161 OC311 at line 598 in file ffcharmmbon.itp, for example) are defined as: OC30P CC3162 CC3161 OC311 3 20.92 41.84 16.74 -41.84 0 0 ; 30P CC3162 CC3161 OC311 1 180 10.46 1 ; 30P CC3162 CC3161 OC311 1 0 8.368 2 ; 30P CC3162 CC3161 OC311 1 0 10.46 3 The commented lines clearly display the multiple definition, that can be described using function 9 3) An other problem rise with impropers dihedrals. Any of them are defined as Ryckaert-Bellemans, ex. HCA1 CC3161 CC3162 OC311 3 0.5858 1.757 0 -2.343 0 0 at line 926 of ffcharmmbon.itp while points 1 and 2 don't impact on the correctness of the simulation and can be bypassed defining [ bondedtypes ] section as following 1 5 321 3 1 0 Problem 3 cannot be solved without manipulating the ffcharmmbon.itp. In fact, since some impropers are defined as functiontype 2 other as functiontype 3, so there is not an unique bondedtypes definition covering both the definition. Did I any mistake or actually there is a problem in the script? Francesco 2012/5/18 Mark Abraham mark.abra...@anu.edu.au On 18/05/2012 2:52 AM, francesco oteri wrote: Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz ( http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion This assumption is no longer valid, is it? As far as I know, infact, now gromacs support multiple periodic function (funtion 9), is it? Correct, but with the inclusion of native CHARMM27 in GROMACS, I have had no reason to upgrade these conversion scripts to support function type 9. 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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
