From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Aug 22 2018 - 13:56:30 CDT
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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