AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jan 25 2008 - 16:48:49 CST

Hi Pankaj,

Bud makes a lot of good points concerning namelist formatting which while
not the problem here I am surprised is not giving you problems, you probably
have a very tolerant fortran compiler.

Concerning the problem you see. This is fixed by Bugfix 26. You need to
apply all the bugfixes to your AMBER code and recompile. See:

http://amber.scripps.edu/bugfixes90.html

This will of course make the code return the real error message which is
that the charge of the QM region is not compatible with number of electrons
in the QM region. So you may need to look more closely at your QM region
selection and make sure it is a reasonable chemical system.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Pankaj R. Daga
> Sent: Friday, January 25, 2008 14:03
> To: amber_at_scripps.edu
> Subject: RE: AMBER: QM/MM: input conversion error
>
> Hi Dr. Dodson,
>
> Thanks for the suggestions. I have modified my input file, as per your
> suggestion. However, the error message is still persisting.
> There is no
> difference in the output file.
>
> Could anyone, please, suggest me the way out?
>
> 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: Friday, January 25, 2008 2:57 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: QM/MM: input conversion error
>
> Pankaj R. Daga wrote:
> > 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
> >
> >
>
> There are several things in your input file that I just do not do the
> way you have done them. I do not know whether they might be the
> source of your problem(s).
>
> First, there are several lines in your &cntrl namelist section that do
> not end with a comma:
> ntp = 1
> cut = 10
>
> My understanding of FORTRAN namelist input is that all namelist items
> MUST be terminated with a comma. I don't know if it is strictly
> necessary, but I even make sure I have a comma on the last namelist
> item:
> ifqnt = 1
> I would write:
> ifqnt = 1,
>
> Secondly, I do not know about your FORTRAN compiler, but I would be
> very suspicious of long input lines. Specifically I am talking bout
> the iqmatoms line. I would break it up so as to be several lines,
> each less than or equal to ~70 characters. E.g.,
> iqmatoms= 1827, 1828, 1829, 1830, 1831, 1832, 3038, 3039, 3040,
> 3041, 3042, 3043, 3050, 3051, 3052, 3053, 3054, 3055,
> 7032, 7033, 7034, 7035, 7036, 7037, 7038, 7039, 7055,
> 7056, 7057, 7058, 7059, 7060, 7061, 7062, 7063, 7064,
> 7065, 7066, 7067, 7068, 7069, 7070, 7071, 7072, 7073,
> 7074, 7075, 7076, 7077, 7078, 7079, 7080, 7081, 7082,
> 7083, 7084, 7085, 7086, 7087, 7088, 7089, 7090, 7091,
> This may not be a problem since it seems to have correctly detected
> nquant = 63.
>
> Note that I have made sure that each line ends in a comma. That is
> just good programming practice, but I have not reviewed the iqmatoms
> parsing code to know if it is necessary. The last item (7091,) does
> need the comma I am pretty sure.
>
> Again, for
> qm_ewald=1, qm_pme=1
> I would write:
> qm_ewald=1, qm_pme=1,
>
> But I do not know whether these are just my personal ways of
> doing things or whether they are necessary. It does seem that the
> variables were correctly picked up from the namelist input, so I
> may just be overly cautious.
>
> The failure seems to be (at least from comparing one of my
> output files)
> at the point were it is going to output the results of its
> determination
> of whether the system is a singlet. At this point one of my jobs has:
>
> QMMM: SINGLET STATE CALCULATION
> QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 72
>
> but your output file does not get that far, ending immediately before
> that output.
>
> I would try these suggestions on a single step run and see if it works
> better, otherwise I have no clue.
>
> 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 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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