AMBER Archive (2005)

Subject: Re: AMBER: About Gaussian Key Words (fwd)

From: Daisuke Katagiri (k-dai_at_graduate.chiba-u.jp)
Date: Mon Apr 11 2005 - 19:03:36 CDT

Dear Duan:

Thank you for your kindly reply.

I retried calculations of the ACE-ALA-NME model with Gaussian03.
Although there was a table of solvent ID in which "Ether" was
equivalent to "13" on their on-line manual, it seems that the key word
of "Solvent=13" means "Toluene" in Gaussian03!!
I think that it is bug.

I think that you told me "Solvent=13" as "Solvent=Ether".
So, I used the following SCRF key words,

#SCRF=(IEFPCM,Solvent=Ether)

Unfortunately, the obtained charges of ALA were still different from
your ff03 charges.

Methods and results are the following.

In the geometry optimizations, the main-chain dihedral angles of alpha
and beta conformer was constrained to (phi, psi)=(-60, -40), (phi,
psi)=(-120, 140), respectively.
*Gaussian03 Key Words : #p opt=ModRedundant hf/6-31g(d,p) (Beta:
(add " 5 7 9 15 -120.0 F" and "7 9 15 17 140.0 F" in ModRedundant input
section) Helix : (add " 5 7 9 15 -60.0 F" and "7 9 15 17 -40.0 F" in
ModRedundant input section))

Single-point calculations were performed about two conformations of
beta and helix, respectively.
*Gaussian03 Key Words : #p rb3lyp/cc-pvtz Geom=checkpoint SCF=tight
Test Pop=mk iop(6/33=2) SCRF=(IEFPCM,Solvent=Ether) guess=read

Then, effective charges were obtained by using RESP method.
I refered to your paper of "J Comput Chem 24: 1999-2012, 2003" and
procedures of 4-Hydroxyl-Proline (PR4).
(http://amber.scripps.edu/antechamber/pro4.html)

ALA
Our charges parm03 charges
N -0.507413 N -0.404773
H 0.308007 H 0.294276
CA 0.040214 CA -0.027733
HA 0.085230 HA 0.120802
CB -0.172112 CB -0.229951
HB1 0.058055 HB1 0.077428
HB2 0.058055 HB2 0.077428
HB3 0.058055 HB3 0.077428
C 0.677949 C 0.570224
O -0.606040 O -0.555129

What is the reason for these differences.
Should I define another Gaussian key words?

I'd appreciate it if any one could tell me the reason for these
differences.

Thank you very much.

Best wishes,

Daisuke

On 2005.4.8, at 08:09 AM, duan_list_at_albert.genomecenter.ucdavis.edu
wrote:

>
> Dear Katagiri:
>
> At the dft stage, you can use,
>
> #SCRF=(IEFPCM, Solvent=13)
>
> The main difference between EPS=4.0 and Solvent=13 is the solvent
> (probe) radius. By default, Gaussian uses water radius. In a sense,
> EPS=4.0 actually mimicks a solvent that is neither water nor ethyl. Its
> polarization effect is close to water instead.
>
> Good luck!
>
> yong duan
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
> Behalf
> Of Katagiri Daisuke
> Sent: Wednesday, April 06, 2005 8:10 PM
> To: amber_at_scripps.edu
> Subject: AMBER: About Gaussian Key Words
>
>
>
> Dear Amber Users,
>
> I am trying to make the charges of new molecules in the same condition
> as ff03 charges.
>
> I understand that I should use the besis sets of HF/6-31G** and
> B3LYP/ccpVTZ for the geometry optimizations and single-point
> calculations, respectively.
>
> And I understand that the IEFPCM method and the Gaussian key word of
> EPS=4.0 should be required only to the single-point calculations.
>
> (I referred to the paper of J Comput Chem 24: 1999-2012, 2003)
>
>
> But I still have any question for the Gaussian key words.
>
> 1. Which Gaussian key words of iop options should I use?
> 2. What values should I use for the RSOLV, DENSITY and EPSINF? 3. Are
> my Gaussian keywords correct?
>
> My Gaussian key words is as following:
> Geometry optimizations : #p opt hf/6-31g(d,p) iop(2/11=1)
> Single-point calculations : #p rb3lyp/cc-pvtz Geom=checkpoint
> SCF=tight Test Pop=mk iop(2/11=1,6/33=2) SCRF=(IEFPCM,Read) guess=read
> *(EPS=4.0 (in the PCM input section))
>
>
> I'd appreciate it if any one could tell me the recommendatory key
> words.
>
>
> Thank you very much.
>
>
> Best wishes,
>
>
> Daisuke
>
>
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------------------------------------------------------------------------
-------------------
Daisuke Katagiri
Graduate School of Pharmaceutical Sciences,
Chiba University
1-33, Yayoi-cho, Inage-ku
Chiba 263-8522
JAPAN

Phone : +81-43-290-2926
Fax : +81-43-290-2925
E-mail : k-dai_at_graduate.chiba-u.jp
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