Re: ADP again

From: Fangqiang Zhu (fzhu_at_ks.uiuc.edu)
Date: Mon Nov 17 2003 - 18:47:59 CST

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 **
> > *****************************************************************
> >
> >
> >

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