[AMBER] A possible bug in t leap when creating topology file ?

From: Arun Srikanth <askforarun.gmail.com>
Date: Wed, 24 Jun 2015 23:59:57 -0400

Hello amber users.

I am attaching the pdb file of the molecule I am working with (1mol.pdb
file contains one molecule, 2mol.pdb contains 2 molecules).

I need to get the amber topology file for 2mol.pdb

(I also have the amber topology file for the single molecule)
The number of dihedral count (including impropers) is 102.

I generated amber topology file for a mixture of two molecules in two


Create a pdb file of two molecules using packmol which is 2mol.pdb. Get the
topology file from amber.

The number of dihedrals in this case is 205


With one mol2 file of the molecule use combine command in tleap to generate
the topology file

The number of dihedrals in this case is 206


I am guessing the dihedral count from both the ways which tleap gives is
wrong. The actual count should be 204.

for example look at the following connectivity information from the
dihedral information generated from parmed.py using the topology files
generated by the above methods. A few commands in matlab such as unique and
accumarray will give you the number of times a dihedral is repeated.

The last column gives the number of times the dihedral is repeated. The
dihedral connectivity from the two topology files are

50 52 55 59 4
58 59 40 61 2
58 59 40 62 2

50 52 55 59 3
58 59 40 61 3
58 59 40 62 3

As you can see that second way (206) gives you one dihedral more than the
first one (205) also the number of time the connectivity that is repeated
is different.

Actually it is supposed look like the following which will give a total
dihedral count of 204 which is the dihedral count obtained by summing up
individual dihedral counts.

50 52 55 59 3
58 59 40 61 2
58 59 40 62 2

It is terribly confusing as which is the right way to generate the topology
file. All three will definitely give different dihedral energies.

Is this a bug in tleap ? or am I making a mistake.


Arun Srikanth (Phd student)
Drexel university

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Received on Wed Jun 24 2015 - 21:30:02 PDT
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