Yes this makes a lot more sense! Thank you so much for your help!
Maria
> The coordinates of frame0.pdb is same as those of frame0.rst. So, I
> assume
> the pdb is from the restart file. In your md input, ntwr=1000 and
> ntpr=500,
> which means that frame0.rst corresponds to the output of NSTEP=1000 and
> the
> rmsd is 5.006. So your rmsd calculated using ptraj should be same as this
> number.
>
> Now, in you ptraj input, I see only single line of rms command.
> It should be
>
> trajin frame0.pdb
> reference origmin.pdb
> rms reference :101-107.CA mass
> rms reference out rmsd.dat (:34-39.CA|:101-107.CA) nofit mass
>
> Please be careful about the second rms command. It has nofit. In the
> first
> rms command above, your molecule is fitted using the mask, :101-107.CA.
> In
> the second rms command, rmsd is calculated without FITTING! That is what
> you meant in your md input file ( tgtfitmask=":101-107.CA",
> tgtrmsmask="(:34-39.CA|:101-107.CA)" ) Also, you should not forget mass
> because targeted md does mass-weighted fitting.
>
> By doing so, I got 5.005 for rmsd. I believe the difference by 0.001 is
> due
> to the truncated coordinates of the pdb file.
>
> I hope it is clear to you.
>
> On Fri, May 14, 2010 at 11:05 AM, <map110.pitt.edu> wrote:
>
>> Hi there,
>>
>> I'm not sure why that happened. I'm attaching frame0.pdb again but it's
>> the complete file. This is what I used for ptraj. I'm also attaching my
>> ptraj.out file.
>>
>> Thanks!
>>
>> Maria
>>
>> > Your frame0.pdb has only 75 atoms. (Is this accidentally truncated??)
>> > This
>> > does not have any atom belong to your mask, :34-39.CA|:101-107.CA.
>> So,
>> it
>> > does not make sense to calculate rmsd without the coordinates.
>> >
>> > On Thu, May 13, 2010 at 4:30 PM, <map110.pitt.edu> wrote:
>> >
>> >> Hi again,
>> >>
>> >> So I'm attaching my ptraj.in file as well as all the files associated
>> >> with
>> >> it. This is the command I used for ptraj:
>> >>
>> >> ptraj orig_nowat.top <ptraj.in> ptraj.out
>> >>
>> >> I should also have mentioned that my system is comprised of a 100
>> >> residue
>> >> receptor and 7 residue peptide fragment ligand and the ligand extends
>> >> the
>> >> anti parallel beta sheet of the receptor upon binding.
>> >> Essentially, we've taken the pdb file for the system (which is also
>> our
>> >> reference structure) and shifted the position of the ligand upwards
>> by
>> >> two
>> >> hydrogen bonds. With the targeted md simulation we want to force the
>> >> conformational change of our structure to the final state (the NMR
>> >> structure). In order to do this, we thought that it would make sense
>> to
>> >> designate tgtfitmask to be the ligand CA atoms and the tgtrmsmask to
>> be
>> >> the ligand CA atoms and the CA atoms from the beta strand of the
>> >> receptor
>> >> which make up the binding interface. Hope this clarifies a few
>> things.
>> >>
>> >> Thanks again!
>> >>
>> >> Maria
>> >>
>> >> > Hi,
>> >> > You also need to provide your script for ptraj. I see your
>> tgtfitmask
>> >> and
>> >> > tgtrmsmask are different. So, I suppose your ptraj script has
>> >> multiple
>> >> > rms
>> >> > commands.
>> >> >
>> >> > On Thu, May 13, 2010 at 3:19 PM, <map110.pitt.edu> wrote:
>> >> >
>> >> >> Hi everyone,
>> >> >>
>> >> >> I'm trying to run a 2 ns targeted md simulation in which the rmsd
>> of
>> >> the
>> >> >> protein structure from the reference structure is gradually
>> reduced
>> >> over
>> >> >> time. In order to test my input files, I ran a 1 ps test
>> simulation
>> >> and
>> >> >> found that there was a discrepancy between the "current RMSD from
>> >> >> reference" given in the .out file and the actual rmsd between the
>> >> >> reference structure and the outputted frame0.rst file (found using
>> >> >> ptraj).
>> >> >> Specifically, in frame0.out the rmsd is 5.124, compared to the
>> actual
>> >> >> rmsd
>> >> >> of 3.28614.
>> >> >>
>> >> >> This is the command I used:
>> >> >>
>> >> >> mpiexec -n 8 nice -19 sander.MPI -0 -i md.in -o frame0.out -p
>> >> >> complex.top
>> >> >> -c eq3.rst -r frame0.rst -x frame0.crd -ref origmin.rst
>> >> >>
>> >> >> I'm also attaching all my input and output files. If anyone has an
>> >> input
>> >> >> on this problem it would be greatly appreciated.
>> >> >>
>> >> >> Thanks in advance for your help!!
>> >> >>
>> >> >> Maria
>> >> >>
>> >> >>
>> >> >> _______________________________________________
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>> >> >>
>> >> >>
>> >> >
>> >> >
>> >> > --
>> >> > Best,
>> >> > InSuk Joung
>> >> > _______________________________________________
>> >> > 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
>> >>
>> >>
>> >
>> >
>> > --
>> > Best,
>> > InSuk Joung
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
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>>
>>
>
>
> --
> Best,
> InSuk Joung
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri May 14 2010 - 11:00:03 PDT
