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From: Aseel Bala <balaahme.msu.edu>

Date: Thu, 12 Jan 2017 13:17:37 -0500

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.

Date: Thu, 12 Jan 2017 13:17:37 -0500

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/amberReceived on Thu Jan 12 2017 - 10:30:03 PST

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