Actually i am confusing about these part of commands can you guide me how i
can produce file that use in these command
HEM = loadmol2 hem.mol2 >>>> HEME coordinate file
CYP = loadmol2 cyp.mol2 >>>> CYS (rename this CYS to CYM) residue to make
coordinate bond with HEME
2j2 = loadpdb CYP2J2.pdb >>>> protein system
set 2j2.460.28 element "Fe"
bond 2j2.460.28 2j2.405.8 >>>> making the bond between HEME and CYS #BOND
CYS-S to HEM-FE
set 2j2.405 connect0 2j2.405.1
set 2j2.405 connect1 2j2.405.9
bond 2j2.404.9 2j2.405.1 #BOND CYS to the protein (new CYP residue)
bond 2j2.405.9 2j2.406.1 #As above
addions 2j2 Na+ 0
solvateoct 2j2 TIP3PBOX 10
saveamberparm 2j2 CYP2J2_FE_box.prmtop CYP2J2_FE_box.inpcrd
regards
On Wed, Jun 28, 2017 at 1:27 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Are you seeing any error messages? Do you have write permission in the
> directory the files are supposed to appear in?
>
> Bill
>
>
> On 6/28/17 10:19 AM, Núbia Prates wrote:
> > Hello,
> >
> >
> > I am using the following command to generate some files during
> equilibrate step:
> >
> >
> > sander -O -i equi_10.in -p complex.top -c heat.rst -r equi_10.rst -o
> equi_10.out -x equi_10.mdcrd -ref heat.rst
> >
> >
> > The problem is that sander do not write the "equi_10.rst" and "
> equi_10.mdcrd" files.
> >
> > Can you help me with that?
> >
> >
> > Regards
> >
> > Nubia
> > _______________________________________________
> > 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
Received on Wed Jun 28 2017 - 11:00:02 PDT
