From: himanshu chandola (beu99419_at_ccsun50.iitd.ernet.in)
Date: Mon Nov 17 2003 - 02:13:25 CST
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 **
> *****************************************************************
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:08 CST