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 3 2 1 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 This assumption is no longer valid, is it?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 list 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. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Cordiali saluti, Dr.Oteri Francesco
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