In the Amber Topology there are two types of arrays used when getting
parameters for certain interactions. For bonds, the first type is two
integer arrays for bonds to hydrogen and bonds to everything else with
the format:
[atom1][atom2][index]...
Where atom1 and atom2 are the atoms involved in the bond, and index is
the index into the second type of array, the parameter arrays:
[Rk0][Rk1]...
[Req0][Req1]...
Here RkX and ReqX are the bond force constant and equilibrium values
respectively. What cpptraj does is update the atoms in bond arrays
(removing any bond for which an atom no longer exists) but does not
modify the index. So for example, given the bond and param arrays:
[atom0][atom1][0][atom0][atom2][1]
[Rk0][Rk1]
[Req0][Req1]
If you strip atom1 the arrays will look like:
[atom0][atom2][1]
[Rk0][Rk1]
[Req0][Req1]
The index for bond atom0-atom2 doesn't change and is still valid since
the parameter arrays are not modified. Rk0 and Req0 are still there
but never accessed. I have done tests and confirmed that stripping a
topology in this way gives the same energy as building the stripped
topology from scratch, it just uses a little more memory.
-Dan
On Tue, Mar 26, 2013 at 8:38 AM, Ignacio J. General <ijgeneral.gmail.com> wrote:
> Thanks Daniel. Just one more question. How is it that the stripped bond
> parameters are still there but not used? Is there some kind of flag telling
> pmemd (or sander) not to use them?
>
> Ignacio
>
>
> On Tue, Mar 26, 2013 at 10:34 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> As of AmberTools 12 cpptraj will write out a fully functional stripped
>> topology file. Any interactions involving stripped atoms are also
>> removed, although the parameters are still there (they are just not
>> accessed).
>>
>> Note that parmed.py also allows you to strip topologies.
>>
>> -Dan
>>
>> On Tue, Mar 26, 2013 at 8:25 AM, Ignacio J. General <ijgeneral.gmail.com>
>> wrote:
>> > Dear Amber users:
>> >
>> > I remember that sometime ago cpptraj was able to strip atoms from the
>> > prmtop file, but it was suggested that we use that only for visualization
>> > purposes, not for simulations. Is this still the case? Or I can use a
>> > stripped prmtop for simulations?
>> >
>> > And in case I can use it for MD, when I strip some residue in a protein,
>> do
>> > I need to first remove the bonds connecting that residue to the others,
>> or
>> > is this done automatically by cpptraj?
>> >
>> > Thanks,
>> >
>> > Ignacio
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Mar 26 2013 - 08:00:05 PDT
