[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.
Thank you all in advance.
Kepa K.
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Received on Tue Sep 18 2012 - 12:00:03 PDT
