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From: Adam Goler (adamgoler_at_gmail.com)
Date: Wed Apr 09 2014 - 20:04:56 CDT
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Hi all,
I'd like to run some NAMD simulations with acetylene molecules in solution.
I have generated a PDB/PSF pair for an acetylene molecule but receive the
following error when solvating:
>Main< (common) 52 % package require solvate
1.5
>Main< (common) 53 % solvate twoCA.psf twoCA.pdb -t 10 -o acetylene_wb
Info) generating solute plus one replica of water...
psfgen) reading structure from psf file twoCA.psf
psfgen) Error processing angles
I assume I made a silly error making the PSF file by hand (likely within
defining the angles). Any help would be appreciated! Thanks!
Adam
----------
----------
I'm defining the atoms in acetylene as follows:
H - C --- C - H
(3) (1) (2) (4)
My PDB looks like:
CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1
ATOM 1 C01 UNK P 1 25.000 24.996 25.000 1.00 0.00 P1
C
ATOM 2 C02 UNK P 1 25.000 26.170 25.000 1.00 0.00 P1
C
ATOM 3 H03 UNK P 1 25.000 23.946 25.000 1.00 0.00 P1
C
ATOM 4 H04 UNK P 1 25.000 27.220 25.000 1.00 0.00 P1
C
END
My PSF looks like:
PSF CMAP
3 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS topology twoCA_autopsf-temp.top
REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }
4 !NATOM
1 U 1 UNK CA CT1 0.160000 12.0110 0
2 U 1 UNK CB CT2 0.160000 12.0110 0
3 U 1 UNK HT1 HC 0.330000 1.0080 0
4 U 1 UNK HT2 HC 0.330000 1.0080 0
5 !NBOND: bonds
1 2 1 3 2 1 2 4
1 2
2 !NTHETA: angles
3 2 1 4
2 !NPHI: dihedrals
3 2 1 4
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0
1 0 !NGRP
0 0 0
-- Adam Goler Graduate Student Fulmer 123C Dept. of Physics and Astronomy Washington State University PO Box 642814 Pullman, WA 99164-2814 Cell Phone: (425) 985 8700 Office Phone: (509) 335 7050 adamgoler.com
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