Re: ADP again

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Nov 17 2003 - 12:58:56 CST

It doesn't matter how the segments are derived, although
covalent bonds should not split accross segments.
To make life easy, protein should be in a protein segment, ions in an ion
segment, ligands in a ligand segment, irregardless of chain ID which
psfgen and namd ignore!

I doubt the way that segments are defined is the cause of your earlier
problem...

On Mon, 17 Nov 2003, himanshu chandola wrote:

> hello,
> I would appreciate if you could answer a specific question about
> generating segments. Say if a hetero atom lies in a particular chain of a
> protein(i.e the chain ids of the hetero atom and the protein chain are the
> same ) do i still put them onto different segments.
>
> regards
>
> 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 Mon, 17 Nov 2003, Brian Bennion wrote:
>
> > 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 **
> > *****************************************************************
> >
> >
> >
>

-- 
*****************************************************************
**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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