AMBER Archive (2004)

Subject: AMBER: Dummy Atoms: How to create them?

From: Ilyas Yildirim (
Date: Thu Dec 30 2004 - 19:23:02 CST

Dear Amber Users,

I want to use the TI method on finding the free energy difference of a
particular system. But I could not understand the procedure on how to
create the files. Let me explain what I have done:

I want to change the carbonyl group of the cytosine with -NH2. In order to
do that I have created a cytosine molecule in .pdb file format with
extra two dummy atom names, DH1 and DH2 which will represents the
hydrogen atoms in the final state. So, I have a pdb file of cytosine
with 2 dummy atoms named DH1 and DH2.

The next step to do was to create the top and crd files in xLeap. What I
have done was;

$ xleap
$ source leaprc.ff99
$ cyto = loadpdb cyto.pdb
$ edit cyto

Here, I have selected the carbonyl group, and edited these atoms:

Name Type Charge Element Pert.type Delta.charge
O2 O -0.6252 O N2 N* (a number)
DH1 0.0000 ? H12 H (a number)
DH2 0.0000 ? H22 H (a number)

Now, when I tried to use;

$ saveamberparmpert cyto cyto.crd

it gives the following error:
> saveamberparmpert cyto cyto.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
WARNING: The perturbed charge: -1.000000 is not zero.
FATAL: Atom .R< 15>.A<DH1 1> does not have a type.
FATAL: Atom .R< 15>.A<DH2 2> does not have a type.
Failed to generate parameters
Parameter file was not saved.
So, it seems that I have to do something else in order to create the
top/crd perturbation files.

I have checked out the mailing list, and tried to find an answer. The
answers given are not easy to understand, and let me explaing what I have
done next.

As far as I understood, we need to first create input files for leap using
antechamber. As I said, I created a cytosine molecule with 2 dummy atoms
named DH1 and DH2 and this file is in .pdb format. (The name of this file
is cyto.pdb) Then I have tried to create a .mol2 file using

$ antechamber -i cyto.pdb -fi pdb -o cyto.mol2 -fo mol2 -nc 0 -c bcc

In the manual, it says that this is the basic prepin file for leap.
Anyways, this did not work. It gave the following error:
c 0 -c bcc

 Unrecognized atomic name DH1 , exit

 Unrecognized atomic name DH1 , exit
 Unrecognized atomic name DH2 , exit
Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C

 Unrecognized atomic name DH1 , exit
 Unrecognized atomic name DH2 , exit
 Unrecognized atomic name DH1, exit
 Unrecognized atomic name DH2, exit
Total number of electrons: 148; net charge: 0

Running: /programs/amber8/exe/divcon
Unable to find mopac charges in divcon.out
 Unrecognized atomic name DH2 , exit
I have tried to create a .prepi file, too, using antechamber, and it gave
the same error.

So, as you can see, I could not prepare the input files for xleap, and as
a result, could not create the files. In the mailing list,
they talk about creating an frcmod file and play with that file such that
xleap will understand the dummy atoms. But as I wrote above, I could not
understand the procedure. I start with a .pdb file (modified such that I
have 2 dummy atom names, DH1 and DH2) and cannot go much. I will
appreciate if someone can tell me what I need to do. Thanks in advance.


Ilyas Yildirim

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