Hi,
Thanks for helping me....I want to know if, I am having two such ligand in
which the charges have countable difference....like if 1stligand+protein
complex is having a charge of 2 Na+ ions and the 2ndligand+protein complex
does not have any charge.
then what can be the solution to such problems..? These charges are added
just for the sake of neutrality.
Thanks in Advance
Regards
On Thu, Jul 8, 2010 at 2:19 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> you can run the two sides of the TI calculation with different net
> charges. Both systems should have the exact same number and ordering of
> the atoms, except for those in scmask. So removing a Cl may be a good
> option, unless you want the transformation ligandA+Cl -> ligandB. This
> depends on your system, i.e. is the extra ion structural or just for
> neutralizing.
>
> Thomas
>
> On Thu, July 8, 2010 4:10 am, sunita gupta wrote:
> > Thanks Thomas I solved that issue....But now I am facing another problem.
> > The two ligands I am dealing with, neutralizes with different no. of Cl-
> > ions. One is having 7 Cl- ions and other one 8, which is causing and
> error
> > "All non-softcore atoms must be identical in both systems"
> > What can be the solutions to this?....Can I remove one Cl- ion of the
> > second
> > one?...
> > Kindly suggest
> > Thanks
> >
> > On Fri, Jul 2, 2010 at 4:13 PM, <steinbrt.rci.rutgers.edu> wrote:
> >
> >> Hi,
> >>
> >> the softcore parts of the ligands can be different, only the common
> >> parts
> >> of the system should have identical coordinates. Since amber stops at
> >> coordinate 1, it probably doesnt reach your ligands. Look at your two
> >> endpoint systems in e.g. vmd, do all atoms except the SC ones align?
> >>
> >> Kind Regards,
> >>
> >> Thomas
> >>
> >> On Fri, July 2, 2010 5:01 am, sunita gupta wrote:
> >> > Thanks Thomas for your reply,
> >> >
> >> > Ya Amber stops at once only one warning....
> >> >
> >> > I understood the concept...but the two ligand I am dealing with are
> >> bit
> >> > different and their coordinates do not match at all. As, these are
> >> docked
> >> > complexes in common protein.
> >> > Can you tell me any way to make their coordinates similar? or any
> >> other
> >> > way
> >> > to solve this problem...?
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On Fri, Jul 2, 2010 at 2:03 PM, <steinbrt.rci.rutgers.edu> wrote:
> >> >
> >> >> Hi,
> >> >>
> >> >> does Amber stop after the warning or does it continue after maybe a
> >> few
> >> >> more warnings?
> >> >>
> >> >> A TI simulation needs all non-softcore atoms to be at the same
> >> >> coordinates
> >> >> in your two systems. Sometimes that is not exactly so, for example
> >> >> because
> >> >> xleap translated the systems origins into their (slightly different)
> >> >> center of masses.
> >> >>
> >> >> sander will realize this and correct small mistakes up to 0.1 A, but
> >> >> warns
> >> >> you that it does so. This is normally not a problem, just a reminder
> >> >> that
> >> >> your system was modified a little bit (which should not change your
> >> >> results).
> >> >>
> >> >> Kind Regards,
> >> >>
> >> >> Thomas
> >> >>
> >> >> On Fri, July 2, 2010 3:43 am, sunita gupta wrote:
> >> >> > Hello Everyone
> >> >> >
> >> >> > I am calculating the relative binding energy of two ligand using
> >> TI. I
> >> >> am
> >> >> > following the tutorial in which benzene was transformed to
> >> phenol.
> >> >> > While Vwd decoupling (second step) I am getting the following
> >> >> > error...."WARNING: Local coordinate 1 differs from partner
> >> >> > coordinate 1 !"
> >> >> >
> >> >> > I have searched the Archive but did not get any help. Does anyone
> >> know
> >> >> > what
> >> >> > does this mean? and how to solve it?
> >> >> > I am using Amber10 and below are my input files
> >> >> > *Min1*
> >> >> > Minimization with restraints
> >> >> > &cntrl
> >> >> > imin = 1, maxcyc = 2000, ntb = 1, ntr = 1, cut = 10.0, ntpr=1,
> >> >> ntx=1,
> >> >> > ntmin=2, icfe=1, klambda=1, clambda=0.95308, ifsc =1, crgmask=
> >> >> > ':DRG.C19,C20,C21,C22,C23,H24,H25,H26,H27,H28,N29,H30,H31,H32',
> >> >> > scmask =
> >> >> ':DRG.C19,C20,C21,C22,C23,H24,H25,H26,H27,H28,N29,H30,H31,H32',
> >> >> > /
> >> >> > Hold the Protein and DRG fixed
> >> >> > 50.0
> >> >> > RES 1 1
> >> >> > END
> >> >> > END
> >> >> >
> >> >> > *Min2*
> >> >> > Minimization with restraints
> >> >> > &cntrl
> >> >> > imin = 1, maxcyc = 2000, ntb = 1, ntr = 1, cut = 10.0, ntpr=1,
> >> >> ntx=1,
> >> >> > ntmin=2, icfe=1, klambda=1, clambda=0.95308, ifsc =1,
> >> >> > crgmask=':DRG.C19,C20,C21,C22,C23,H24,H25,H26,H27,H28',
> >> >> > scmask = ':DRG.C19,C20,C21,C22,C23,H24,H25,H26,H27,H28',
> >> >> > /
> >> >> > Hold the Protein and DRG fixed
> >> >> > 50.0
> >> >> > RES 1 1
> >> >> > END
> >> >> > END
> >> >> >
> >> >> > *Group File *
> >> >> > -O -i min1_0.95308 -p new3z.top -o min1_0.95308.out -c new3z.crd -r
> >> >> > min1_0.95308.crd -x min1_0.95308.mdcrd -ref new3z.crd
> >> >> > -O -i min2_0.95308 -p new54z.top -o min2_0.95308.out -c new54z.crd
> >> -r
> >> >> > min2_0.95308.crd -x min2_0.95308.mdcrd -ref new54z.crd
> >> >> >
> >> >> > Thanks in Advance
> >> >> > --
> >> >> > SUNITA GUPTA
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
> >> >>
> >> >> Dr. Thomas Steinbrecher
> >> >> BioMaps Institute
> >> >> Rutgers University
> >> >> 610 Taylor Rd.
> >> >> Piscataway, NJ 08854
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > SUNITA GUPTA
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >> Dr. Thomas Steinbrecher
> >> BioMaps Institute
> >> Rutgers University
> >> 610 Taylor Rd.
> >> Piscataway, NJ 08854
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > --
> > SUNITA GUPTA
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
SUNITA GUPTA
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Received on Fri Jul 09 2010 - 05:30:05 PDT
