I took a PDB file that had some missing residues, and added them using
swisspdb viewer. I'm attempting to slowly heat up the structure, as to
allow things to carefully reposition themselves.
I'm attempting this in implicit (I tried explicit but that didn't go so
well either) using this as my MD input
&cntrl
imin=0,irest=0,
nstlim=10000,dt=0.0001,
ntpr=10,ntwx=10,
ntt=3,gamma_ln=10.0,
tempi=0.0,temp0=50.0,
ntb=0,igb=1,
cut=999.0, rgbmax=999.0,
restraintmask='!:WAT&.CA,C,O,N',
restraint_wt=10.0,
ntr=1,
/
On Mon, Apr 22, 2013 at 5:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Without knowing exactly what you are trying to do it's difficult to
> tell what may be going wrong. Does your trajectory contain box
> coordinates (i.e. were you using GB, PME, etc) and is it ASCII
> (ioutfm=0) or NetCDF (ioutfm=1)? What format are you using to try and
> load the trajectory into VMD? Does the topology you are using in VMD
> match the trajectory (i.e. have you stripped waters etc)?
>
> -Dan
>
> On Mon, Apr 22, 2013 at 1:50 PM, Jonathan Gough
> <jonathan.d.gough.gmail.com> wrote:
> > Thanks Hai,
> >
> > That worked, but when I load the trajectory, it's a ridiculous mess.
> Still
> > not sure what's wrong. thoughts?
> >
> >
> > On Mon, Apr 22, 2013 at 3:15 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> >> Have you tried loading inpcrd as a restart file into VMD?
> >>
> >> Hai
> >>
> >>
> >> On Mon, Apr 22, 2013 at 11:50 AM, Jonathan Gough <
> >> jonathan.d.gough.gmail.com
> >> > wrote:
> >>
> >> > Dear peoples,
> >> >
> >> > I took a pdb, cleaned it up. loaded it into leap, saved a pdb, saved
> the
> >> > inpcrd and prmtop files.
> >> >
> >> > When I load the pdb, everything is fine. when I lod the inpcrd and
> >> prmtop,
> >> > it looks like a single Nitrogen is stretched out into infinity...
> >> >
> >> > I can't seem to figure out what the deal is. obviously (maybe)
> >> attempting
> >> > minimization or heating or anything else makes a huge mess.
> >> >
> >> > Does anyone have any insight as to where I am making the mistake?
> >> >
> >> > I can provide lots more details if it's not an obvious error.
> >> >
> >> > Thank,
> >> > Jonathan
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 22 2013 - 14:30:04 PDT
