Re: TMD RMSD problem

From: Elif Ozkirimli (ozkiriml_at_gmail.com)
Date: Fri Apr 10 2009 - 15:50:50 CDT

Ali, thanks for the reply.
I am performing the alignment based on the TMD residues in VMD. I have tried
all sorts of alignment combinations. However, the disagreement between VMD
and NAMD is not the only problem. The namd output never falls below 2 even
though I can clearly see that the TMD residues have reached their target
conformation.

Does anybody have a working TMD input file so that I can compare with my
input file. I must be setting something wrong in the input file since
everybody else seems to be happy about the RMSD results.

Elif.

On Fri, Apr 10, 2009 at 9:27 PM, Ali Emileh <ali.emileh_at_gmail.com> wrote:

> Elif,
> I'm not sure if this might help or not, but NAMD TMD does the alignment
> only on the TMD residues (i.e. the ones labeled
> for forcing). So the resultant alignment would be different from a whole
> molecule one. So what I would suggest is do the
> alignment only on the TMD atoms and then measure RMSDs for each frame. When
> I do that, I can clearly "see" the small
> TMD reported RMSDs in VMD. I haven't measured it, but I'm guessing it would
> be very close to TMD RMSDs.
>
>
> On Thu, Apr 9, 2009 at 12:24 PM, Elif Ozkirimli <ozkiriml_at_gmail.com>wrote:
>
>> Thanks for the responses.
>> I am aligning all frames in the dcd before I calculate the RMSD. The
>> indexing of the atoms is also correct and the same in VMD and NAMD.
>>
>> I forgot to mention: the RMSD in the NAMD output never falls below 2 (the
>> RMSDref does fall to 0) but when you wach the simulation in VMD it's obvious
>> that the TMD is complete and the protein has assumed the target conf.
>>
>> Elif.
>>
>>
>>
>> On Wed, Apr 8, 2009 at 11:35 PM, Joshua Adelman <jadelman_at_berkeley.edu>wrote:
>>
>>> Are you aligning all of the frames in your trajectory before you
>>> calculate the RMSD? If not the results will surely be different since namd
>>> performs the alignment when it calculates the tmd force and outputs the
>>> rmsd
>>> Josh
>>>
>>>
>>> On Apr 8, 2009, at 1:21 PM, Elif Ozkirimli wrote:
>>>
>>> Dear all,
>>>
>>> I am trying to use TMD to move a protein from one conformation to the
>>> other. I read the initial coordinates and then the target coordinates are
>>> read within the TMD section with the correct occupancy values. RMSD values
>>> are reported in the NAMD output file. I then try to calculate RMSD vs time
>>> for the same coordinate set using VMD. However, the RMSD values in the NAMD
>>> output file and those I calculate from VMD are different. Does anybody else
>>> have the same problem?
>>>
>>> I had poster earlier about this problem. I was hoping 2.7 would fix this
>>> but alas it does not.
>>> Any help or suggestions would be greatly appreciated.
>>>
>>> Elif.
>>>
>>>
>>> ------------------------------------------------------------------------------------------------------
>>> Joshua L. Adelman
>>> Biophysics Graduate Group Lab: 510.643.2159
>>> 218 Wellman Hall Fax: 510.642.7428
>>> University of California, Berkeley
>>> http://nature.berkeley.edu/~jadelman
>>> Berkeley, CA 94720 USA jadelman_at_berkeley.edu
>>>
>>> ------------------------------------------------------------------------------------------------------
>>>
>>>
>>>
>>
>

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