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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
M. L. Dodson
Sent: Thursday, January 24, 2008 1:25 PM
To: amber.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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of
> M. L. Dodson
> Sent: Thursday, January 24, 2008 12:32 PM
> To: amber.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
Received on Sun Jan 27 2008 - 06:07:31 PST
