From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Feb 09 2010 - 06:07:22 CST
I case anyone has a similar problem:
The error of dihedral angles for dihedral anlges that have multiple cosine
components. XPLOR/CHARMM writes multiple dihedral bonds in to the PSF, while
NAMD writes only one dihedral bond and extracts multiple dihedral terms
directly from the parameter file.
The only solution I found was to set up the system again using NAMD/psfgen.
The bonds with zero force constants are H-H bonds CHARMM uses for rigid
water.
It's all written in the tutorial (one just has to read it very carefully:)
Best regards,
Ajasja
On Tue, Nov 24, 2009 at 13:47, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>wrote:
> Hello,
>
> I have search the mailing list for related problems, but none of the
> threads seem to offer a conclusive solution.
>
> NAMD exits with the following message:
>
> FATAL ERROR: Multiplicity of Paramters for diehedral bond C NH1 CT1 C of 1
> exceeded
>
> This is probably related to the topology file for the MTSL spin label
> (residue CMTS in the psf file), but for the life of me, I cannot figure out,
> where the dihedral is duplicated.
> The psf file was generated with CHARMM and written using "write psf card
> xplor" at BOMLEV -1.
>
> What would be the best way to find the duplicated dihedral angle? Could I
> perhaps just make NAMD ignore the multiplicity?
>
>
> PS: should I be concerned about the following NAMD warnings?
>
> Warning: Ignored 5860 bonds with zero force constants.
> Warning: Will get H-H distance in rigid H2O from H-O-H angle.
>
>
> I have attached the following files:
> ekvinatoksin.log -- the log file form NAMD
> ekvinatoksin.start.1ns.conf -- the NAMD configuration file
> par_all27_prot_lipid_pf.inp -- CHARMM27 parameter file
> top_all27_prot_lipid_pf.inp -- CHARMM27 topology file
> top_cmtssl2_c22_pf.inp -- topology file of the spin label
> write_namd_psf.inp -- Charmm inputfile used to generate the PSF
> write_namd_psf.inp -- Charmm output file of the PSF generation
> weqii-i18c.namd.psf -- the resulting problematic PSF file
>
>
> Thank you for your help & best regards,
> Ajasja Ljubetic
>
>
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