AMBER Archive (2008)

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

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Thu Jan 24 2008 - 13:25:03 CST

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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