# Re: [AMBER] Sander input into Gaussian

From: Aseel Bala <balaahme.msu.edu>
Date: Thu, 12 Jan 2017 16:02:07 -0500

No I am not doing a single-point calculation. I was doing a frequency
calculation in the case I included previously.
As for the rigid shift, when I compare the coordinates in inpcrd versus the
ones Gaussian is given, there is a rigid shift. In the sample I discussed in
the last email. The X,Y and Z coordinates given to Gaussian are shifted by
+0.130133, +0.180033,+0.278667 compared to the inpcrd ones.

However, starting with a different box, I see that, while there is a rigid
shift of all the molecules in the new box as well, they are shifted by a
different amount (0.028533,-0.1202,0.1641 compared to that inpcrd).

I am trying to generate my own input into Gaussian manually. This is why I
am interested in figuring out exactly what how sander alters the coordinates
and charges to create the input.
I hope this clarified a few issues.
Thanks again.

```--
Aseel Bala Ahmed
PhD Candidate, Chemical Engineering
Michigan State University
-----Original Message-----
Sent: Thursday, January 12, 2017 1:24 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Sander input into Gaussian
Aseel
I am a bit confused regarding your questions.
First, what you see is NOT a z-matrix, but rather a regular Cartesian set of
coordinates.
Second, are you doing a single point calculation or different calculation?
Third, if you visualize the coordinates from inpcrd and the one gaussian is
using, do you see just a rigid shift ?
As for the charges, the values in the prmtop are in a different set of units
than in gaussian or what we consider standard charge units. This is done to
make the computations faster inside amber. The best way to find out what the
real charges are, is to use Parmed to study the prmtop.
On 1/12/17 1:17 PM, Aseel Bala wrote:
> Hello,
> Thank you for your response.
> Yes I am aware of that tutorial and have used it to guide me. However,
> the authors do not describe how the numbers in the Z-matrix are
> generated by sander. I can see that in their example the numbers are
> similar (but not
> identical) to those in the inpcrd file for atoms 11-21. However, in my
> case that is not at all what I get.
>
> The QM molecule has the following coordinates in the inpcrd file in my
case:
>
> C	1.8931333  -0.4644667   0.9476667
> C	0.6781333  -0.6684667  -0.0083333
> C	-0.3438667   0.4715333  -0.0603333
> C	 -1.6998667   0.1375333  -0.5243333
> O	-2.3958667   1.3245333  -0.7943333
> H	-1.7828667   1.8985333  -1.2593333
> H	2.6561333  -1.1524667   0.5826667
> H	1.6591333  -0.7204667   1.9806667
> H	2.3121333   0.5355333   0.8386667
> H	0.1331333  -1.5384667   0.3556667
> H	0.9841333  -0.9144667  -1.0253333
> H	-0.4238667   0.8645333   0.9526667
> H	0.0761333   1.1825333  -0.7723333
> H	-1.5468667  -0.4604667  -1.4233333
> H	-2.1988667  -0.4954667   0.2096667
>
> In contrast, the Z matrix generated for the molecule is:
> C         1.7629999999999992      -0.6445000000000007
> 0.6690000000000013
> C         0.5479999999999994      -0.8485000000000007
> -0.2869999999999987
> C        -0.4740000000000007       0.2914999999999993
> -0.3389999999999986
> C        -1.8300000000000007      -0.0425000000000007
> -0.8029999999999987
> O        -2.5260000000000002       1.1444999999999992
> -1.0729999999999986
> H        -1.9130000000000005       1.7184999999999993
> -1.5379999999999985
> H         2.5259999999999994      -1.3325000000000007
> 0.3040000000000012
> H         1.5289999999999992      -0.9005000000000007
> 1.7020000000000013
> H         2.1819999999999995       0.3554999999999993
> 0.5600000000000012
> H         0.0029999999999993      -1.7185000000000008
> 0.0770000000000013
> H         0.8539999999999993      -1.0945000000000007
> -1.3039999999999985
> H        -0.5540000000000007       0.6844999999999992
> 0.6740000000000012
> H        -0.0540000000000007       1.0024999999999995
> -1.0509999999999988
> H        -1.6770000000000007      -0.6405000000000007
> -1.7019999999999984
> H        -2.3290000000000006      -0.6755000000000007
> -0.0689999999999987
>
> I don't know why the coordinates are so different in my case. Any help
> is appreciated.
>
> Thanks again.
> --
>
> Aseel Bala Ahmed
> PhD Candidate, Chemical Engineering
> Michigan State University
>
>
> -----Original Message-----
> From: Huang Jing [mailto:jing.huang8911.gmail.com]
> Sent: Wednesday, January 11, 2017 5:33 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Sander input into Gaussian
>
> The tutorial:
> http://nf.nci.org.au/~vvv900/monash/amber-gaussian/index.html
>
> jing
>
> On Wed, Jan 11, 2017 at 11:55 PM, Aseel Bala <balaahme.msu.edu> wrote:
>
>> Hi everyone,
>>
>>
>>
>> I am using the sander interface to run a QM calculation on one
>> molecule
>> (Butanol- 15 atoms) in a box. I am including other molecules whose
>> have atoms that fall within a certain distance around the QM molecule
>> as point charges.
>>
>>
>>
>> My input to sander (qm.in) looks as follows:
>>
>> Testing tutorial on website for QMMM with Gaussian
>>
>> &cntrl
>>
>> imin=0,nstlim = 0,   !do not run a minimization or MD run
>>
>> ntb=2,          !constant pressure periodic boundary conditions
>>
>> ntf=2,ntc=2,
>>
>> cut=10.0,       !10 ang classic bond cutoff
>>
>> ntp=1,
>>
>> ifqnt=1         !switch on QM/MM
>>
>> &end
>>
>> &qmmm
>>
>>
>> qmcharge=0,
>>
>> qm_theory='EXTERN',
>>
>> qmcut=10.0,
>>
>> qm_ewald = 0 !Use a real-space cutoff for QM-QM and QM-MM long range
>> interactions.
>>
>> &end
>>
>> &gau
>>
>> method = 'B3LYP',
>>
>> basis = '6-31G* Freq',
>>
>> &end
>>
>>
>>
>> Atoms 16-30 here belong to the molecule that I want to calculate
>> quantum mechanically. Then I run the command:
>>
>>
>>
>> sander -O -i qm2.in -o qm2.out -c ../../c2.inpcrd -p
>> ../../../simbox.prmtop
>>
>>
>>
>> I get several outputs including the file that sander used as an input
>> to Gaussian which I attached here (old.gau.job.inp). The beginning of
>> the file looks like this:
>>
>> %chk=gau_job.chk
>>
>> %NProcShared=1
>>
>> %mem=256MB
>>
>> #P B3LYP/6-31G* Freq SCF=(Conver=8) NoSymm Charge Prop=(Field,Read)
>>
>>
>>
>> Gaussian run using SANDER external interface.
>>
>>
>>
>> 0 1
>>
>> C         1.7629999999999992      -0.6445000000000007
>> 0.6690000000000013
>>
>> C         0.5479999999999994      -0.8485000000000007
>> -0.2869999999999987
>>
>> C        -0.4740000000000007       0.2914999999999993
>> -0.3389999999999986
>>
>> C        -1.8300000000000007      -0.0425000000000007
>> -0.8029999999999987
>>
>> O        -2.5260000000000002       1.1444999999999992
>> -1.0729999999999986
>>
>> H        -1.9130000000000005       1.7184999999999993
>> -1.5379999999999985
>>
>> H         2.5259999999999994      -1.3325000000000007
>> 0.3040000000000012
>>
>> H         1.5289999999999992      -0.9005000000000007
>> 1.7020000000000013
>>
>> H         2.1819999999999995       0.3554999999999993
>> 0.5600000000000012
>>
>> H         0.0029999999999993      -1.7185000000000008
>> 0.0770000000000013
>>
>> H         0.8539999999999993      -1.0945000000000007
>> -1.3039999999999985
>>
>> H        -0.5540000000000007       0.6844999999999992
>> 0.6740000000000012
>>
>> H        -0.0540000000000007       1.0024999999999995
>> -1.0509999999999988
>>
>> H        -1.6770000000000007      -0.6405000000000007
>> -1.7019999999999984
>>
>> H        -2.3290000000000006      -0.6755000000000007
>> -0.0689999999999987
>>
>>
>>
>>    11.6699999999999999   1.8194999999999990   2.9420000000000011
>> 0.0914000055333610
>>
>>    10.7509999999999994   1.7334999999999996   1.8860000000000012
>> -0.5467999944666389
>>
>>     9.9049999999999994   1.5534999999999992   2.3030000000000013
>> 0.4050000055333611
>>
>>    11.4599999999999991   2.8114999999999992   3.3430000000000013
>> 0.0112000055333610
>>
>>    11.5770000000000000   1.0224999999999993   3.6800000000000010
>> 0.0112000055333610
>>
>>     7.9059999999999988  -3.2045000000000008   1.3910000000000013
>> -0.1850999944666389
>>
>>     8.1440000000000001  -2.2615000000000007   2.5240000000000009
>> 0.0026000055333610
>>
>>     7.8429999999999991  -0.7435000000000007   2.2410000000000014
>> -0.2023999944666389
>>
>> ...
>>
>>
>>
>> >From what I saw online, this file starts off with a symbolic Z
>> >matrix
>> which
>> should state the Cartesian coordinates of the atoms in the QM region
>> (top set of lines) and then the coordinates (and charge) of all the
>> atoms considered as point charges (second set of lines).
>>
>>
>>
>> The issue is that there seems to be a manipulation of the coordinates
>> before this file is formed because these numbers do not match with
>> the coordinates in the inpcrd I give sander for neither the QM atoms
>> or the point charges.
>> I
>> also don't know how the charges are being calculated in this file
>> since they also don't match the prmtop file I included in the input.
>>
>>
>>
>> Does anyone know how the input to Gaussian is generated by sander? I
>> am attaching all my files in this email in case they might help.
>>
>> I would really appreciate any insight into this.
>>
>>
>>
>> Thanks everyone,
>>
>> --
>>
>>
>>
>> Aseel Bala Ahmed
>>
>> PhD Candidate, Chemical Engineering
>>
>> Michigan State University
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
> --
> ----------------------
> Dr. Jing Huang
> *Institute of Chemistry and the Lise Meitner-Minerva Center for
> Computational Quantum* *Chemistry, Hebrew University of Jerusalem,
> Givat Ram Campus, Jerusalem 91904, Israel*
> _______________________________________________
> AMBER mailing list
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>
>
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--
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Jan 12 2017 - 13:30:03 PST
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