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
>> >>
>> >>
>> >> _______________________________________________
>> >> 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
>> 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
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: ptraj.out
Received on Fri May 14 2010 - 08:30:03 PDT
