AMBER Archive (2008)

Subject: RE: AMBER: QM/MM: input conversion error

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Fri Jan 25 2008 - 14:11:24 CST

Dear Dr. Dodson and Dr. Walker,

 

Thanks for your suggestion. I could make overcome the error message.
However, I have new error message after I use modified input file.

 

This time error message is

 

"forrtl: severe (60): infinite format loop, unit 6, file
/user_path/QMMM1/eqlb3.out"

 

I searched for the error in the output file. However, I could not locate,
where I was going wrong. The input files works fine for the molecular
mechanics simulation. I am attaching the input file and output file along
with.

 

I would appreciate if someone can help me sorting out the problem.

 

Thanks and Regards

 

Pankaj

 

===============================================================

If your ship doesn't come in, swim out to it...Jonathan Winters

===============================================================

Pankaj R. Daga |

Dept. of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu

417 Faser Hall, | fax: +1-662-915-5638

University of Mississippi | phone: +1-662-915-1853

University, MS, 38677-1848 |

===============================================================

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
M. L. Dodson
Sent: Thursday, January 24, 2008 1:25 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: QM/MM: input conversion error

 

Pankaj R. Daga wrote:

> Dear Dr. Dodson,

>

> Thanks for the suggestion. However, even after changing the input file, I
am

> facing same error.

>

> The error message mentions the position of mistake. "line 23, position
57"

> The line 23 in the input file is

>

> iqmatoms= '@3038-3043, 3050-3055, 7028-7039, 7053-7105',

>

> Could you please suggest the way out?

>

> Thanks and Regards

>

> Pankaj

>

 

Well, I never quote (') or use @ in my iqmatoms list. Maybe leave

them out? I think iqmatoms is just a comma-separated list of QM

atoms. That is the way I specify it in my simulations, and they seem

to work just fine. Ross or Gustavo can correct me if I am wrong.

 

Bud Dodson

 

>

> -----Original Message-----

> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of

> M. L. Dodson

> Sent: Thursday, January 24, 2008 12:32 PM

> To: amber_at_scripps.edu

> Subject: Re: AMBER: QM/MM: input conversion error

>

> Pankaj R. Daga wrote:

>> Dear Amber community,

>>

>>

>>

>> I am trying to run QM/MM MD simulations using amber9. I have carried out

>> initial steps (Minimize / heat / equilibrate) system with pure classical

>> mechanics (Thanks to Gustavo for his suggestions). Now I am trying to

>> run equilibration using QM/MM. However, I am facing one error message

>> with the input file. The error is as reported below:

>>

>>

>>

>> forrtl: severe (64): input conversion error, unit 5, file /XXX/eqlb3.in,

>> line 23, position 57

>>

>>

>>

>> Here is input file, I am using for the simulations:

>>

>>

>>

>> QM/MM Equillibration Run

>>

>> &cntrl

>>

>> imin=0,

>>

>> irest=1,

>>

>> ntx=7,

>>

>> ntb = 2,

>>

>> ntp = 1

>>

>> ntr=0,

>>

>> ntc=1,

>>

>> ntf=1,

>>

>> tempi=300.00,

>>

>> temp0=300.00,

>>

>> ntt=3,

>>

>> gamma_ln=1.0,

>>

>> nstlim = 5000, dt= 0.002,

>>

>> ntpr = 50,

>>

>> ntwx = 50,

>>

>> ntwr = 50,

>>

>> cut = 10

>>

>> ifqnt = 1

>>

>> /

>>

>> &qmmm

>>

>> iqmatoms= '@3038-3043, 3050-3055, 7028-7039, 7053-7105',

>>

>> qmcharge=0,

>>

>> spin = 1

>

> You left the comma of the preceeding line.

>

>> qmtheory=1,

>>

>> qmshake=1,

>>

>> qm_ewald=1, qm_pme=1

>>

>> /

>>

>>

>>

>> I have checked with the character at (line 23, position 57), however, I

>> could not understand, what was going wrong with that.

>>

>>

>>

>> Could you please let me know, there is something wrong in my input file?

>>

>>

>>

>> Your suggestions will be very helpful to me.

>>

>>

>>

>> Thanks and Regards

>>

>>

>>

>> Pankaj

 

  

-- 

M. L. Dodson

Business Email: activesitedynamics-at-comcast-dot-net

Personal Email:   mldodson-at-comcast-dot-net

Phone:      eight_three_two-56_three-386_one

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  • application/octet-stream attachment: eqlb3.in
  • application/octet-stream attachment: eqlb3.out

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