[gmx-users] (no subject)

[Justin Lemkul]

On 7/14/14, 6:17 AM, Yana Tsoneva wrote:
> Dear colleagues,
>
>
>
> Firstly, I want to thank Justin Lemkul for helping me on the topic
> "polarizable water and non-polarizable alkanes". Now I have to
> simulate systems that consist of polarizable water and polarizable alkanes.
> The chosen force field is CHARMM with Drude oscillators.
>
> I am trying to use the python script cgenff_charmm2gmx.py to generate the
> needed files, but the following error occurs:
>
>
>
> NOTE1: Code tested with python 2.7.3. Your version: 2.6.6 (r266:84292, Jan
> 22 2014, 09:42:36)
>
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]
>
> 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  charmm36-mar2014.ff//forcefield.doc :
> 2b8
>
> NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include
> parameters that are already in CGenFF' option when uploading a molecule into
>
> CGenFF.
>
> error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top
>
> 17 0
>
>
>
> I found that another person had this problem, but I still could not fix it.
> I have attached the files I am using. The command line I enter is:
>
> ./cgenff_charmm2gmx.py PENT pentane.mol2
> ./drude_toppar_oct13/toppar_drude_model_2013a.str charmm36-mar2014.ff
>
>
>
> I will really appreciate if someone could help me,
>

The CGenFF conversion script is intended to process a .mol2 file with a single 
molecule and a corresponding .str file with a single molecule.  What you're 
trying to do is doomed to fail for two reasons:

1. The toppar_drude_model_2013a.str file contains all model compounds we used in 
the parametrization of the Drude FF
2. CHARMM36 from March 2014 is an additive force field.

Please also note that our parametrization of the Drude FF is with thermalized, 
mass-bearing Drude particles.  In principle, these types of systems can be 
simulated in Gromacs using an SCF procedure to solve the positions of the Drude 
particles, but not out of the box in the case of mass-bearing Drudes.  I am 
working on implementing all of the necessary algorithms to make this a reality, 
but the code is not yet suitable for public consumption.  Using massless 
Drudes/shells will work fine, but strictly speaking that is not the Drude FF 
that we have parametrized.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================