From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Aug 10 2011 - 00:00:55 CDT
The problem lies in the extra H-H bond in TIP3 water in the topology file.
Psfgen doesn't care about the ANGLE lines in the topology file and instead
creates angles for every set of three bonded atoms and dihedrals for every
set of four. If you comment out the "H1 H2" part of the BOND line under
TIP3, you should find everything works fine.
As an aside, you might want to try CHARMM36 lipids, if you haven't already.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Jernej Zidar
Sent: Tuesday, August 09, 2011 11:48 PM
Subject: Re: namd-l: Custom CHARMM forcefield usage problem
I think I have solved the problem.
The PSFGEN utility in VMD apparently failed to process the
After recreating the PSF/PDB files within the Charmm program and
taking care to write an xplor PSF file everything appears to be in
On Wed, Aug 10, 2011 at 12:12, Jernej Zidar <jernej.zidar_at_gmail.com> wrote:
> Years ago we developed a CHARMM force field for lipids, that works
> flawlessly within the program CHARMM. When I try to use it in NAMD
> though NAMD complains about:
> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CEL1 CTL1 (ATOMS 8 39)
> In Charmm I would generally set the input like so:
> !read topology
> open read card unit 10 name top_all27_lipid.rtf
> read rtf card unit 10
> close unit 10
> !read parameters
> open read card unit 10 name par_all27_lipid.prm
> read param card unit 10
> close unit 10
> stream toppar_all27_lipid_cholesterol.str
> In NAMD I'm using only the par_all27_lipid.prm file for NAMD
> complains if I try to use the stream
> toppar_all27_lipid_cholesterol.str in the conf file:
> parameters par_all27_lipid.prm
> parameters toppar_all27_lipid_cholesterol.str
> The error I get is:
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (ATOMS 44641
> 44643 44642)
> I created the PSF and PDB files for the simulation using the PSFGEN
> tool within VMD and using the aforementioned force field files.
> Any tips on how to solve this will be much appreciated.
> Jernej Zidar
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