On Tue, Sep 18, 2012 at 2:51 PM, Kepa K. Burusco <kekoburgo.yahoo.es> wrote:
> [18-IX-2012]
>
> Hi Everybody,
>
> I am trying to run a test. A couple of TI calculations for for the alpha
> => beta anomeric transformation for glucose (glycam06h): one in gas phase
> and the other one in water. Since it is my first TI calculation I am
> following the Amber Tutorial 9.
>
> When creating the input files for the the gas phase I followed the next
> steps:
>
> 1) tleap first run:
> I created the topology, coordinates and PDB files for the alpha and beta
> steps running the script "createFiles_stp01" (attached). Everething was OK.
>
> 2) tleap second run:
> I renamed the "glaVAC.pdb" as "glaComVAC.pdb" and deleted the "unique
> atoms" (ROH hydroxyl group and H1 atom, in both alpha and beta states) to
> obtain a new PDB just containing the common atoms for both states.
> Then I copied the "glaComVAC.pdb" into "glbComVAC.pdb" and changed the
> residue name from "0GA" to "0GB" in the column so all cartesian
> coordinates, atom numbers and order of atoms would be the same for both
> files (the tutorial says that the coordinates and order must be the same).
> Then I called tleap with the second script "createFiles_stp02" (also
> attached) to load the new PDB files and create the topology and coordinate
> files for the TI run.
> And then, checking the new files I discovered that the atoms of the ROH
> group were missing (as I wanted) BUT tleap automatically added the hydrogen
> atom H1 (info_tleap files atached).
>
> Did I do anything wrong in the process? Can anyone help me in this point?
> It seems that when people do this process in the tutorial, tleap just write
> the new files not adding any missing hydrogen to the benzene or the phenyl.
>
tleap adds all atoms to a residue that are in the residue template you
loaded. Tleap doesn't know anything about 'typical' connectivity or common
chemistry -- it will read in a library of residues and associate each
residue (given a name) with the list of atoms and bonds that are defined in
that library. If your input structure does not have all of the atoms
present in the library, it adds them.
Therefore, if you want a new residue that does *not* have a hydrogen atom,
you will need to create a new residue (with a different name) and make sure
you use that residue's name wherever you want it located.
HTH,
Jason
>
> Thank you all in advance.
>
> Kepa K.
>
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>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Sep 18 2012 - 13:00:02 PDT
