AMBER Archive (2004)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
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 pert.top/crd 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.name 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.top cyto.crd

it gives the following error:
------------------------------------------
> saveamberparmpert cyto cyto.top 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 pert.top/crd 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.

Sincerely,

Ilyas Yildirim

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