Re: CGenFF 4.1 lone pairs

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Aug 22 2018 - 17:37:57 CDT

Hi Jeff,

Correct, this is not currently supported but on our to-do list.

Brian

On Wed, Aug 22, 2018, 2:58 PM Jeff Comer <jeffcomer_at_gmail.com> wrote:

> Recent versions of the CHARMM General Force Field include lone pairs to
> represent halogen bonds ( http://doi.org/10.1016/j.bmc.2016.06.034 ). I
> know NAMD supports lone pairs for Drude, but I run into problems when I try
> to use the CGenFF lone pairs.
>
> As an example, I generated a psf file for chlorobenzene (called CHLB in
> top_all36_cgenff.rtf) using CHARMM (Free Version 43b1). When I try to run a
> simulation with this psf in NAMD
> (NAMD_Git-2018-08-21_Linux-x86_64-multicore), I get the error:
>
> FATAL ERROR: BAD FORMAT FOR LPHOST LINE 1 IN PSF FILE LINE
> LINE=2 1 F 1.64000 0.00000 0.00000
>
> Older versions of NAMD (2.12) don't give an error, but the lone pair
> floats around and clearly doesn't behave correctly.
>
> Is CGenFF 4.1 not fully supported by NAMD? Recently, the ParamChem CGenFF
> webserver ( http://cgenff.paramchem.org ) upgraded to CGenFF 4.1, so this
> could be a major problem for combining CGenFF and NAMD.
>
> For reference, here's my psf file:
>
> PSF EXT CMAP CHEQ XPLOR
>
> 2 !NTITLE
> * NONE
> *
> * DATE: 8/22/18 13:42:34 CREATED BY USER:
> comer
>
> 13 !NATOM
> 1 ADSB 1 CHLB C1 CG2R61 -0.100000
> 12.0110 0 0.00000 -0.301140E-02
> 2 ADSB 1 CHLB H1 HGR62 0.150000
> 1.00800 0 0.00000 -0.301140E-02
> 3 ADSB 1 CHLB C2 CG2R61 -0.115000
> 12.0110 0 0.00000 -0.301140E-02
> 4 ADSB 1 CHLB H2 HGR61 0.115000
> 1.00800 0 0.00000 -0.301140E-02
> 5 ADSB 1 CHLB C3 CG2R61 -0.115000
> 12.0110 0 0.00000 -0.301140E-02
> 6 ADSB 1 CHLB H3 HGR61 0.115000
> 1.00800 0 0.00000 -0.301140E-02
> 7 ADSB 1 CHLB C4 CG2R61 -0.115000
> 12.0110 0 0.00000 -0.301140E-02
> 8 ADSB 1 CHLB H4 HGR61 0.115000
> 1.00800 0 0.00000 -0.301140E-02
> 9 ADSB 1 CHLB C5 CG2R61 -0.100000
> 12.0110 0 0.00000 -0.301140E-02
> 10 ADSB 1 CHLB H5 HGR62 0.150000
> 1.00800 0 0.00000 -0.301140E-02
> 11 ADSB 1 CHLB C6 CG2R61 0.600000E-01
> 12.0110 0 0.00000 -0.301140E-02
> 12 ADSB 1 CHLB CL CLGR1 -0.210000
> 35.4530 0 0.00000 -0.301140E-02
> 13 ADSB 1 CHLB LP LPH 0.500000E-01
> 0.00000 -1 0.00000 -0.301140E-02
>
> 13 !NBOND: bonds
> 1 2 1 3 3 4
> 3 5
> 5 6 5 7 7 8
> 7 9
> 9 10 9 11 11 1
> 11 12
> 12 13
>
> 18 !NTHETA: angles
> 2 1 3 2 1 11
> 3 1 11
> 1 3 4 1 3 5
> 4 3 5
> 3 5 6 3 5 7
> 6 5 7
> 5 7 8 5 7 9
> 8 7 9
> 7 9 10 7 9 11
> 10 9 11
> 1 11 9 1 11 12
> 9 11 12
>
> 24 !NPHI: dihedrals
> 1 3 5 6 1 3
> 5 7
> 1 11 9 7 1 11
> 9 10
> 2 1 3 4 2 1
> 3 5
> 2 1 11 9 2 1
> 11 12
> 3 1 11 9 3 1
> 11 12
> 3 5 7 8 3 5
> 7 9
> 4 3 1 11 4 3
> 5 6
> 4 3 5 7 5 3
> 1 11
> 5 7 9 10 5 7
> 9 11
> 6 5 7 8 6 5
> 7 9
> 7 9 11 12 8 7
> 9 10
> 8 7 9 11 10 9
> 11 12
>
> 0 !NIMPHI: impropers
>
>
> 0 !NDON: donors
>
>
> 0 !NACC: acceptors
>
>
> 0 !NNB
>
> 0 0 0 0 0 0
> 0 0
> 0 0 0 0 0
>
> 1 0 !NGRP NST2
> 0 1 0
>
> 1 !MOLNT
> 1 1 1 1 1 1
> 1 1
> 1 1 1 1 1
>
> 1 3 !NUMLP NUMLPH
> 2 1 F 1.64000 0.00000 0.00000
> 13 12 11
>
> 0 !NCRTERM: cross-terms
>
>
>
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website: http://jeffcomer.us
>

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