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
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Received on Thu Jul 08 2010 - 01:30:03 PDT
