AMBER Archive (2006)

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

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Tue Nov 28 2006 - 17:47:19 CST

For gaussian, which base set has Zn? I know there are
several base sets, but one source says the 6-31G* can
recognize Zn.

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

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

> 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.
>
=== message truncated ===

 
____________________________________________________________________________________
Yahoo! Music Unlimited
Access over 1 million songs.
http://music.yahoo.com/unlimited
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu