AMBER Archive (2009)

Subject: Re: [AMBER] Gly -> Ala mutation

From: manoj singh (mks.amber_at_gmail.com)
Date: Mon Nov 09 2009 - 10:26:00 CST

Dear Prof. Roitberg.

Thanks for the reply.

The problem in mutating the trajectories by changing it into pdb file
is when I am reading the pdb file again, the Leap is adding new
hydrogen which will consequently need minimization and the trajectory
will be no more be same.

However, I found a way to do this. What I did is I created a new
residue where I added a dummy (no charge no vdW parameters) atom
connected to one of the hydrogen of the Gly. Now I am running the
simulation and at the end I will give the position of hydrogen as the
pointer of CB and position of dummy as pointer of CG. I hope this will
fix my problem.

Manoj

On Mon, Nov 9, 2009 at 11:13 AM, Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:
> Dear Manoj.
>
> As Jason mentioned, there is no way to change it with mmpbsa.pl
>
> you can write a pdb file, modify it by hand, read it into tleap to get a new
> prmtop.
>
> Changing your trajectory for those new coordinates requires some pretty
> advanced scripting, but you need to do it by hand.
>
> manoj singh wrote:
>>
>> Dear Prof. Simmerling,
>>
>> Thanks for the reply.
>>
>> The Gly I want to mutate has the plenty of space around it and its phi
>> and psi are in most stable conformation.
>>
>> How exactly can I make this mutation using mm_pbsa.pl or any other method.
>>
>> I will be very thankful for your kind response.
>>
>> Manoj
>>
>>
>> On Mon, Nov 9, 2009 at 10:13 AM, Carlos Simmerling
>> <carlos.simmerling_at_gmail.com> wrote:
>>>
>>> Leap uses the connectivity tree information in the library about bond
>>> lengths, angles and default dihedral angles. making Gly into Ala is
>>> straightforward in the sense that there is no ambiguity about where to
>>> put
>>> the heavy atoms, but as Jason said it may well be that there is no room
>>> for
>>> the Cbeta, and in reality the structure would relax to accommodate it.
>>> instead you might get unreasonably high energies.
>>>
>>>
>>> On Sun, Nov 8, 2009 at 3:16 PM, Jason Swails <jason.swails_at_gmail.com>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> There are no scripts in the amber distribution that will do this
>>>> mutation
>>>> for MM-PBSA to use with alanine scanning.  The only way to make this
>>>> mutation is to create a PDB (you can use ambpdb), change GLY to ALA at
>>>> the
>>>> desired residue (deleting the hydrogens attached to CA) and loading the
>>>> structure into leap.  Leap will add the other atoms, but I don't know
>>>> what
>>>> algorithm it uses to do so.
>>>>
>>>> Good luck,
>>>> Jason
>>>>
>>>> On Sun, Nov 8, 2009 at 2:14 PM, manoj singh <mks.amber_at_gmail.com> wrote:
>>>>
>>>>> Thanks for your reply.
>>>>>
>>>>> I understand the Gly can attain all PHI and PSI values, however other
>>>>
>>>> amino
>>>>>
>>>>> acids can not. But, if the Gly is in "usual" conformation, is it
>>>>> possible
>>>>> to
>>>>> mutate it to Ala using any available technique/script in the process of
>>>>> performing MM-PBSA.
>>>>>
>>>>> One more thing, when talking about electrostatic energy, one should not
>>>>> forget desolvation energy.
>>>>>
>>>>> Manoj
>>>>>
>>>>>
>>>>> On Sun, Nov 8, 2009 at 12:53 PM, Jason Swails <jason.swails_at_gmail.com
>>>>>>
>>>>>> wrote:
>>>>>> Hello,
>>>>>>
>>>>>> You can write your own script/program to do the transformation.  Soon
>>>>>
>>>>> there
>>>>>>
>>>>>> will be a release of a new MM-PB(GB)SA script for amber that should be
>>>>>> faster and more user-friendly (and should handle alanine-scanning more
>>>>>> easily).  However, even this new script does not handle Gly-Ala
>>>>
>>>> mutations
>>>>>>
>>>>>> since this is more complex than every other mutation.  For every other
>>>>>> residue, all that is needed to handle an alanine mutation is to remove
>>>>>> extraneous atoms and readjust some bond lengths to match those in
>>>>>
>>>>> alanine.
>>>>>>
>>>>>> Glycine is the only amino acid that has fewer atoms than alanine, so
>>>>>> in
>>>>>> order to perform that mutation, atoms would need to be added to the
>>>>>
>>>>> system.
>>>>>>
>>>>>> This is non-trivial, because the question becomes "where do we add
>>>>
>>>> those
>>>>>>
>>>>>> extra atoms?" (Ala has more degrees of freedom than Gly)
>>>>>>
>>>>>> It may even be the case that in a specific conformation, an alanine
>>>>
>>>> would
>>>>>>
>>>>>> not even fit where there's a glycine, so you would get an unphysically
>>>>>
>>>>> high
>>>>>>
>>>>>> penalty for mutating that residue.  Thus, the short version, there is
>>>>
>>>> no
>>>>>>
>>>>>> clear-cut, systematic way to handle a Gly->Ala mutation, so it's not
>>>>>
>>>>> done.
>>>>>>
>>>>>> Furthermore, alanine scanning is designed more to measure the
>>>>>
>>>>> electrostatic
>>>>>>
>>>>>> (and perhaps VDW) effects that a particular sidechain has on the
>>>>
>>>> activity
>>>>>>
>>>>>> of
>>>>>> a protein.  Glycine (and proline, though Pro->Ala is an allowed
>>>>
>>>> mutation
>>>>>
>>>>> in
>>>>>>
>>>>>> the upcoming version if not this one) more often serves a role in
>>>>>> modulating
>>>>>> the structure of a protein, so alanine scanning is often ill-suited to
>>>>>> probing the importance of a Glycine in the first place.
>>>>>>
>>>>>> Hope this helps,
>>>>>> Jason
>>>>>>
>>>>>> On Sun, Nov 8, 2009 at 12:25 PM, manoj singh <mks.amber_at_gmail.com>
>>>>>
>>>>> wrote:
>>>>>>>
>>>>>>> Hi all!
>>>>>>>
>>>>>>> The mm_pbsa.pl can't do Gly->Ala mutation. Is there any way to do
>>>>
>>>> this
>>>>>>>
>>>>>>> mutation in trajectory.
>>>>>>>
>>>>>>> Sincerely,
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER_at_ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ---------------------------------------
>>>>>> Jason M. Swails
>>>>>> Quantum Theory Project,
>>>>>> University of Florida
>>>>>> Ph.D. Graduate Student
>>>>>> 352-392-4032
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER_at_ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER_at_ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>> --
>>>> ---------------------------------------
>>>> Jason M. Swails
>>>> Quantum Theory Project,
>>>> University of Florida
>>>> Ph.D. Graduate Student
>>>> 352-392-4032
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER_at_ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> --
>                           Dr. Adrian E. Roitberg
>                             Associate Professor
>                            Quantum Theory Project
>                           Department of Chemistry
>
>                 Senior Editor. Journal of Physical Chemistry
>                          American Chemical Society
>
> University of Florida                         PHONE 352 392-6972
> P.O. Box 118435                               FAX   352 392-8722
> Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber