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
Received on Fri Jul 02 2010 - 04:00:05 PDT
