[AMBER] Creating an AMBER input to Gaussian

From: Aseel Bala <balaahme.msu.edu>
Date: Thu, 6 Oct 2016 12:27:00 -0400

Hello,

I am working on setting up a QM/MM simulation and have been following a
tutorial on how to create the Gaussian input file.

My situation is unique, however, because I will want to begin my simulation
from a specific frame in a previous MD simulation. Therefore, I do not want
to minimize the energy again before running the QM/MM simulation.

 

My sander input file (qmmm_in.in) is:

Testing tutorial on website for QMMM with Gaussian

 &cntrl

  ifqnt=1

 &end

&qmmm

  qmmask=':31',

  qmcharge=0,

  qm_theory='EXTERN',

  qmcut=15.0

 &end

&gau

   method = BLYP,

   basis = 6-31G,

   charge = 0,

&end

 

I was able to extract the coordinates of the molecules for the frame I am
interested in and tried to write my own inpcrd file to input with sander:

The file (frame3302.inpcrd) had the format as follows:

 

default

    4530

9.5220000 7.7680000 25.2830000 9.9890000 7.1480000 26.5680000

11.2810000 7.7970000 26.9740000 11.8220000 7.1260000 28.2400000

12.5300000 5.9010000 27.8530000 11.9050000 5.5240000 27.2280000

8.7930000 7.0870000 24.8430000 9.0200000 8.7330000 25.3530000

..

35.4780000 35.5360000 35.5240000

 

Where the first line is an arbitrary title, the second is the number of
atoms in the frame and the other lines have the x,y,z coordinates of each
atom with 6 decimal places. The last line contains size of the periodic box.
I followed the format for inpcrd here
(http://ambermd.org/formats.html#restart) to create this file.
 
The problem is when I run sander from the command line:
        sander -O -i qmmm_in.in -o qmmm.out -c frame3302.inpcrd -p
simbox.prmtop -r qmmm.rst

 

I get the following in the output file:

 

 

-------------------------------------------------------

Amber 14 SANDER 2014

-------------------------------------------------------

 

[-O]verwriting output

 

File Assignments:

| MDIN: qmmm_in.in

| MDOUT: qmmm.out

|INPCRD: frame3302.inpcrd

| PARM: simbox.prmtop

|RESTRT: qmmm.rst

| REFC: refc

| MDVEL: mdvel

| MDFRC: mdfrc

| MDEN: mden

| MDCRD: mdcrd

|MDINFO: mdinfo

| MTMD: mtmd

|INPDIP: inpdip

|RSTDIP: rstdip

|INPTRA: inptraj

 

 

Here is the input file:

 

Testing tutorial on website for QMMM with Gaussian

&cntrl

ifqnt=1

&end

&qmmm

qmmask=':31',

qmcharge=0,

qm_theory='EXTERN',

qmcut=15.0

&end

&gau

method = BLYP,

basis = 6-31G,

charge = 0,

&end

 

----------------------------------------------------------------------------
----
1.  RESOURCE   USE:
----------------------------------------------------------------------------
----
 
| Flags:
getting new box info from bottom of inpcrd
|  INFO: Old style inpcrd file read
 
ERROR: Problem reading coordinates or velocities from frame3302.inpcrd
 
I could not understand line     3 :
9.5220000 7.7680000 25.2830000 9.9890000 7.1480000 26.5680000
 
 
I'm not seeing what I am doing wrong. Any help with this will be very much
appreciated. If I have forgotten to mention any important information,
please let me know.
Thank you very much,
 
--
 
Aseel Bala 
PhD Candidate, Chemical Engineering
Michigan State University
 



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Received on Thu Oct 06 2016 - 09:30:02 PDT
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