Date: Wed, 28 Jun 2017 13:49:53 -0400
HEM = loadmol2 hem.mol2 >>>> HEME coordinate file
when i run the above command error come hem.mol2 not find { i thought that
this code read the hem coordinate from the protein system that contain
heme rather then i create separate file for hem.mol } and in the lower
commands show about bonding between heme and cys
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
On Wed, Jun 28, 2017 at 1:34 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > can you guide me how i can produce file that use in these command
>
> Try searching the web for them, also if you name each one you need, that
> will help people.
>
> Bill
>
>
> On 6/28/17 10:30 AM, Rana Rehan Khalid wrote:
> > 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
> >>> _______________________________________________
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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