VMD-L Mailing List

From: Adam Goler (adamgoler_at_gmail.com)
Date: Wed Apr 09 2014 - 20:04:56 CDT

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