Dear Thomas Evangelidis,
As you said, I have looked at CPPTRAJ/PTRAJ in AmbeTools12 for an option to
convert .prmtop file to a .psf file. Unfortunately, I couldn't able to find
any action command in AmberTools12 for converting amber topology file to a
psf file. Is there any other way I can do this conversion?
Waiting you valuable reply
Thanks in advance
Regards,
Anu
On Wed, Dec 11, 2013 at 4:39 PM, anu chandra <anu80125.gmail.com> wrote:
> Hi,
>
> Thanks to all for the valuable suggestions. I will carefully look in to
> your replies.
>
> Thanks once again.
>
> Regards
> Anu
>
>
> On Wed, Dec 11, 2013 at 2:56 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> BTW: careful with PCAs...
>>
>> First, make sure that the PCAs you choose represent a substantial amount
>> of the variance. Too many papers show 1 or 2 PCAS and the sum of them is
>> only 20% of the variance. Granted, it is the top 20%, but even then, it
>> is a small part of the story.
>>
>> Second, PCAS are notoriously hard to converge. Do this: take your 75 ns
>> MD, split in into 2 halves. Redo PCA for each half separately and see if
>> the first PCA vector for one half is similar to the first PCA vector for
>> the second one. If not, then your PCA vecotr for the free energy is very
>> arbitrary and does not tell you too much about your system.
>>
>> Adrian
>>
>> On 12/10/13 3:59 PM, Thomas Evangelidis wrote:
>> > Carma does what Jason described automatically, namely you can plot the
>> Free
>> > Energy along two or three Principal Components. All you need is to
>> convert
>> > your .prmtop/.nc to .psf/.dcd with cpptraj from AmberTools. Check it
>> out:
>> >
>> > http://utopia.duth.gr/~glykos/Carma.html
>> >
>> > HTH,
>> > Thomas
>> >
>> >
>> >
>> > On 10 December 2013 22:45, Jason Swails <jason.swails.gmail.com> wrote:
>> >
>> >> On Tue, Dec 10, 2013 at 5:23 AM, anu chandra <anu80125.gmail.com>
>> wrote:
>> >>
>> >>> Dear Amber users,
>> >>>
>> >>>
>> >>> I am working with all-atom MD simulations of protein-ligand system. I
>> >> have
>> >>> carried out PCA analysis after 75ns of simulation. By looking at the
>> >>> collective motions along the first principle component, I could able
>> to
>> >> see
>> >>> that the protein is visiting two different conformations.Now, I am
>> >> looking
>> >>> for a method to capture the free energy landscape of these
>> conformational
>> >>> changes. If I am right, usual methodologies like meta-dynamics. AMD
>> etc.
>> >>> are usually used to overcome the high energy barrier during the
>> >>> conformational changes. Since I could capture the conformational
>> changes
>> >> in
>> >>> my protein during the classical MD itself, it seems like the energy
>> >> barrier
>> >>> is too low between these two different conformations. How can I
>> capture
>> >>> free energy change during these conformational changes? Which method
>> will
>> >>> be helpful for me to do this calculation?
>> >>>
>> >> If you have sufficient sampling without using any type of biasing
>> >> potential, you can just calculate free energies directly from the
>> >> simulation.
>> >>
>> >> This is typically done using a histogram along whatever reaction
>> coordinate
>> >> you choose to define and taking the negative log of the histogram
>> >> population (divided by the population of the most populated bin if you
>> want
>> >> to set the minimum energy to 0). Multiplied by -kT, of course...
>> >>
>> >> Good luck,
>> >> Jason
>> >>
>> >> --
>> >> Jason M. Swails
>> >> BioMaPS,
>> >> Rutgers University
>> >> Postdoctoral Researcher
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>>
>> --
>> Dr. Adrian E. Roitberg
>>
>> Colonel Allan R. and Margaret G. Crow Term Professor.
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Dec 20 2013 - 01:00:03 PST
