AMBER Archive (2006)

Subject: AMBER: RE: Amber: ZN-complex file

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Nov 28 2006 - 17:21:40 CST

I am not sure why you cannot generate prep input file from your mol2
file. Here is the prep input file I generated for your mol2 file

    0 0 2

This is a remark line
molecule.res
CYM INT 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 O o M 3 2 1 1.540 111.208 180.000 0.000000
   5 C c1 M 4 3 2 1.214 29.840 -89.431 0.000000
   6 CA c3 M 5 4 3 1.530 121.213 78.992 0.000000
   7 N n2 S 6 5 4 1.489 109.095 -56.942 0.000000
   8 HN hn E 7 6 5 1.010 118.294 112.177 0.000000
   9 HA h1 E 6 5 4 1.081 109.519 -176.803 0.000000
  10 CB c3 M 6 5 4 1.531 109.649 63.056 0.000000
  11 HHB h1 E 10 6 5 1.079 109.421 -70.186 0.000000
  12 H1 h1 E 10 6 5 1.080 109.393 169.843 0.000000
  13 SG ss M 10 6 5 1.810 109.622 49.873 0.000000
  14 Zn Zn M 13 10 6 2.303 107.790 -175.598 0.000000

LOOP

IMPROPER

DONE
STOP

The command I used was antechamber -fi mol2 -fo prepi -i ZN_CYM.mol2 -o
zn.prepi -j 0

I used -j 0 since I know that bond type cannot handle metallic molecules
properly. You need to make sure that the atom types in the mol2 file are
correct.

As to your gaussian calculations, you need to use another basis set
other than 6-31G* which has parameters for Zn.

Once you get the prep input file, you may run parmchk to find the
missing parameters. Those related to bond lengths and bond angles may be
easily found in the output of the ab initio calculation. The torsional
angle parameters involved by Zn may be simply set to 0.0 if you can not
find proper ones. However, if it is the case, you must be very cautious
to make sure that the MD structures are rescannable.

All the best

Junmei

-----Original Message-----
From: Fenghui Fan [mailto:fenghui_fan_at_yahoo.com]
Sent: Sunday, November 26, 2006 12:50 PM
To: Junmei Wang
Subject: RE: Amber: ZN-complex file

Hi,

Attached is a mol2 file which I got from the PDB file.
Then I tried to get the prepin file and the frcmod
file. As you suggested, in each command of Antechamber
I suppose -j 0.

For step 5:

5) run antechamber to get prep input files: read in
input.ac and
gaussian.crg to get a prep input file (antechamber
-fi ac -c rc -cf
gaussian.crg -fo prepi -o input.prepi)),

will you please tell me whether input.ac is from your
step 2 input.ac or the gaussian.ac from your step 4?

I have tried both, but the prepin file and the frcmod
are almost empty.

Then for your step 5 I tried to use gaussian.out from
your step 3 as the input file, and it almost work, but
in the prepin file, it lacks the information of ZN and
two other atoms (See attached), and it the frcmod file
it lacks the information on ZN.

Will you please tell me how to solve this problem? I
just take the ZN_CYM as an example to learn the
methods to get the parameters.

Best regards.

Fenghui Fan

--- Junmei Wang <jwang_at_encysive.com> wrote:

> You may convert your pdb file to an ac or mol2 file,
> manually add bonds
> formed by Zn. Then (2) run antechamber to get
> gaussian input file
> input.ac (-fo gcrt), manually modify the gaussian
> input file to use
> proper basis set (the default one may not have
> parameters for Zn); (3)
> run gaussian to get gaussian output; (4) run
> antechamber to get resp
> charges (antechamber -fi gout -i gaussian.out -c
> resp -fo ac -o
> gaussian.ac; antechamber -fi ac -c rc -cf
> gaussian.crg -i gaussian.ac);
> (5) run antechamber to get prep input files: read in
> input.ac and
> gaussian.crg to get a prep input file (antechamber
> -fi ac -c rc -cf
> gaussian.crg -fo prepi -o input.prepi)); (6) run
> parmchk to get missing
> parameters, you may need manually provide some force
> field parameters
> (you can get most bond and angle parameters from
> gaussian calculations)
>
> Good luck
>
> Junmei
>
>
> ==================================================
> Dr. Junmei Wang
> Chemistry & Biophysics
> Encysive Pharmaceuticals Inc.
> 7000 Fannin, Houston TX 77030
> Tel: 713-578-6649
> Email: jwang_at_encysive.com
>
http://amber.scripps.edu/antechamber/antechamber.html
> ==================================================
>
>
> -----Original Message-----
> From: Fenghui Fan [mailto:fenghui_fan_at_yahoo.com]
> Sent: Monday, November 13, 2006 9:21 AM
> To: Junmei Wang
> Subject: Amber: ZN-complex file
>
>
> Dr. Junmei Wang,
>
> Attached is a PDB file with Zn coordinated by 4 CYS.
>
> Will you please show me the right process to edit
> the
> attached PDB file, get its charge and get the prepin
> file by Antechamber?
>
> I am looking forward to getting your reply.
>
> Best regards.
>
> Fenghui Fan
>
>
>
>
>
________________________________________________________________________
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