[gmx-users] CGenff parameters in gromacs but missing in charmm package

[Justin Lemkul]

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.

> 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.

-Justin

> 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.

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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