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From: Adrian Roitberg <roitberg.ufl.edu>

Date: Thu, 12 Jan 2017 13:23:48 -0500

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.

adrian

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
*

*>>
*

*>> qmmask='.16-30',
*

*>>
*

*>> 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
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

Date: Thu, 12 Jan 2017 13:23:48 -0500

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.

adrian

On 1/12/17 1:17 PM, Aseel Bala wrote:

-- Dr. Adrian E. Roitberg University of Florida Research Foundation Professor. Department of Chemistry University of Florida roitberg.ufl.edu 352-392-6972 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jan 12 2017 - 10:30:03 PST

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