Dear Justin, > On 4/17/18 3:34 AM, Fabian Keller wrote: >> Dear all, >> I am using the CGenFF/paramchem framework for a new molecule (an imidazolium >> cation derivative with methyl groups on both N atoms). >> I faced a known problem going from CHARMM package to Gromacs with parameters >> already existing in CHARMM for Gromacs. I assume that this is due to >> paramchem only being implemented for CGenFF3.0.1 and Gromacs using version >> 4.1. > > That's precisely your problem. The CGenFF server is using an old > version, and therefore it finds bonded parameters that need to be > guessed by analogy. In fact, CGenFF 4.0 has these parameters and they > are the values you should use. So for all of the parameters that are > being overridden, remove them from your .prm file before #including it > in the topology. The optimized parameters in CGenFF 4.0 are what you > want, and they're all already there in ffbonded.itp.
Okay thanks, this is what I did. I just was not sure wether the approach was appropriate. >> I wanted now to check if the parameters exist in the CGenFF for CHARMM and >> they don?t! > > I'm finding them. It's impossible for grompp to say something is in > ffbonded.itp if it isn't. Be sure you're considering forward and reverse > orders of atom types when you're searching for them. Yes, sure you find them in the charmm36-jul2017.ff/ffbonded.itp, but they are missing in the CGenFF version for CHARMM the toppar_c36_jul17/par_all36_cgenff.prm file (both the latest release). So why is there a discrepancy, or is it even a discrepancy or rather something I am missing here? > >> How is it possible that the parameters exist in the Gromacs version of >> CHARMM force-field >> (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz >> >> <http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz>) >> while they are missing in the CHARMM FF version >> (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz >> >> <http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz>)? >> Why are the dihedrals considered duplicate, when the atomtypes clearly are >> different? Is this due to CHARMM handling dihedral potentials differently to >> Gromacs? >> >> Following the link you find all used parameter and force field files >> (https://www.dropbox.com/sh/m89q64g0pae6wrf/AAAx1aNtJ1TZKNDFgUo2oSu7a?dl=0 >> <https://www.dropbox.com/sh/m89q64g0pae6wrf/AAAx1aNtJ1TZKNDFgUo2oSu7a?dl=0>) >> and in the following the error output. >> Thank you very much for all hints and help! >> Best wishes, >> Fabian >> >> >> >> >> >> >> WARNING 1 [file chim.prm, line 4]: >> Overriding Bond parameters. >> >> old: 0.1468 276144 0.1468 276144 >> new: CG334 NG2R52 1 0.14530000 251040.00 >> >> >> WARNING 2 [file chim.prm, line 11]: >> Overriding U-B parameters. >> >> old: 107 351.456 0 0 107 351.456 >> 0 0 >> new: NG2R52 CG334 HGA3 5 110.100000 351.456000 0.00000000 >> 0.00 >> >> >> WARNING 3 [file chim.prm, line 13]: >> Overriding U-B parameters. >> >> old: 126.3 368.192 0.243 19246.4 >> 126.3 368.192 0.243 19246.4 >> new: CG2R53 NG2R52 CG334 5 127.100000 209.200000 0.20900000 >> 12552.00 >> >> >> ERROR 1 [file chim.prm, line 25]: >> 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. >> >> >> ERROR 2 [file chim.prm, line 26]: >> 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. Thanks a lot, Fabian -- 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 [email protected].
