Re: ADP again

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 19 2003 - 11:00:40 CST

Nope,

in the most recent versions those atoms are CN7 CN7B and CN7B
the sugar is the same whether the base has changed or not!!

On Tue, 18 Nov 2003, Fangqiang Zhu wrote:

> If you look at residue ADP or ATP in that file, you'll find that atoms C2', C3',
> and C4' are all of the type CN7, and there's an angle for the three, therefore
> the CN7-CN7-CN7 angle parameters are needed.
>
> In other nucleotide residues, C2' is of type CN7B, instead of CN7. So I guess
> if you change its type in ADP to CN7B, the complaint should go away.
> However I'm not sure whether that's the right thing to do or not...
>
> Zhu
>
>
> Brian Bennion wrote:
>
> > 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 **
> > *****************************************************************
>

-- 
*****************************************************************
**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) 424-6605                 **
*****************************************************************

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