Re: ADP again

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Nov 18 2003 - 10:24:33 CST

Why not just look it up and fix it?? From the top_all27_prot_na.inp that I
downloaded from MacKerells website I don't see a problem. The carbons in
the sugar ring are all named sufficiently different so that no CN7-CN7-CN7
angle would ever exist...

Brian

On Mon, 17 Nov 2003, Fangqiang Zhu wrote:

> Hi,
>
> As far as I know, other people also encountered similar problems when
> using CHARMM27 force field to simulate ADP or ATP. There seems to be
> some typos in either "top_all27_prot_na.inp" or "par_all27_prot_na.inp" file
> regarding these two residues.
>
> I'd suggest that you email Alexander MacKerell, Jr. (the major developer
> of CHARMM force field) to report this problem (i.e., the CN7-CN7-CN7
> angle is not defined in the parameter file).
>
> Zhu
>
>
> 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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