From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Nov 17 2003 - 11:18:09 CST
hello,
Himanshu,
you need to figure out why these errors are occuring or you will not learn
anything. There is no workaround for learning the basics of MD.
Take some time and study the organization of the parameter file and
topology file and how your starting structure is read by psfgen.
The error is in the pdb file you used in psfgen, which then generates a
psf file that doesn't make sense with namd and par_all27_prot_na.inp
Brian
On Mon, 17 Nov 2003, himanshu chandola wrote:
> hello,
> changing to par_all27_prot_na.inp did help matters as such that the
> error came at a later level(ANGLE CN7 CN7 CN7 not found). But still i get
> an error in namd initialization.
>
> any workarounds please?
>
> as stated earlier this error is coming when i am having a protein having
> ADP as one of the heteroatoms. I have put all heteroatoms in separate
> chains. Like if MG comes in chain I of the protein and ADP comes in the
> chain F of the protein - then there are separate segments for the hetero
> atoms themselves i.e MG and ADP being put in separate segments while
> protein according to its chains.
>
>
> himanshu
>
> ----------------------------------------
> Morpheus: Do you believe in fate, Neo?
> Neo: No.
> Morpheus: Why Not?
> Neo: Because I don't like the idea that I'm not in control of my life.
>
>
> On Sat, 15 Nov 2003, Brian Bennion wrote:
>
> > you can change the name of the parameter file that namd reads in the namd
> > config file...
> > change the 22 to 27 in the line that states par_all27_prot_lipid.inp
> >
> > Brian
> >
> > On Sun, 16 Nov 2003, himanshu chandola wrote:
> >
> > > Dear all,
> > > I am again stuck with ADP. I can generate the psf file thanks to
> > > the ADP parameters in the charmm 27 param file. But when i use the
> > > correspondingly generated files for namd - i have this CN7 atom in the
> > > ADP which is not in the charmm 22 file (i guess namd only accepts charmm
> > > 19 and 22 param files). So i encounter an error.
> > >
> > > Any workarounds please ?
> > >
> > > himanshu
> > >
> > > ----------------------------------------
> > > Morpheus: Do you believe in fate, Neo?
> > > Neo: No.
> > > Morpheus: Why Not?
> > > Neo: Because I don't like the idea that I'm not in control of my life.
> > >
> > >
> >
> > --
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 422-6605 **
> > *****************************************************************
> >
> >
> >
>
-- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 422-6605 ** *****************************************************************
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