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
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Received on Thu May 13 2010 - 14:00:03 PDT
