Dear Dr. Thomas Steinbrecher
Thanks for your reply.
As you said, if I build a single pdb-file of my system with water and ions,
how to change GC base pair to AT?
Thanks in advance.
On Sun, Feb 19, 2012 at 4:35 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > this process: 21890 atoms, partner process: 23383 atoms
> > SANDER BOMB in subroutine setup_sc
> > All non-softcore atoms must be identical in both systems
> [...]
> > Since number of Na ions for neutrality of the both systems is the same,
> > this difference in number of atoms corresponds to water molecules.
>
> You cannot build the two end states independently. All atoms, except the
> ones in your scmasks must be identical in their starting positions and
> order in the prmtop. It may be easiest to built a single pdb-file of your
> system with water and ions and read it into leap twice, just changing the
> residue name or something similar to build V0 and V1.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Sun Feb 19 2012 - 06:30:02 PST
