[gmx-users] protein-DNA simulation with Amber port

[TJ Piggot]

Hi

I have just checked again by trying to set up a run again using spc/e with 
amber03. I still get this same error. I am sure the order in the [ 
molecules ] section is correct, and it is the same order as in the .top 
file with tip3p or tip4p which both work fine. The only difference between 
the setup's is the -water option given to pdb2gmx and the -cs option in 
genbox

Tom

--On Friday, June 01, 2007 14:59:53 +0200 Erik Marklund 
<erikm at xray.bmc.uu.se> wrote:

> spc/e works fine for me with ffAMBER03. Are you sure the ordering of
> your top-file is correct? Check that the [ molecules ] section in
> correctly ordered.
>
> 1 jun 2007 kl. 14.55 skrev TJ Piggot:
>
>> Hi,
>>
>> If i remember correctly i also got this error with spc (and spc/e)
>> and the ffamber port. However i was only playing around in testing
>> different water models and did not spend ages trying to fix this
>> problem because i use tip3p or tip4p for most of my runs.
>>
>> So as to the error i am not sure, however if you try one of the
>> tip*p water models i think that you should not get this error
>> (remember to have #include
>> ffamber_tip*p in your .top file).
>>
>> Sorry i can't be of more help
>>
>> Tom
>>
>> --On Friday, June 01, 2007 01:25:22 -0700 Alaguraj Veluchamy
>> <alaguraj_v at yahoo.com> wrote:
>>
>>> Dear Gmx-users,
>>> I have followed  http://folding.stanford.edu/ffamber/ for porting
>>> amber
>>> in Gromacs and i am trying to simulate protein-DNA complex.
>>> Preprocessing
>>> the topology files gives error as below:
>>>
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22#
>>> checking input for internal consistency...
>>> calling /lib/cpp -traditional...
>>> processing topology...
>>> Generated 2628 of the 2628 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 0.5
>>> Generated 2628 of the 2628 1-4 parameter combinations
>>> Cleaning up temporary file gromppkzsTQq
>>> Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line
>>> 41 ]:
>>>              Atom index (1) in settles out of bounds (1-0)
>>>
>>> I checked at the spc.itp file and found that the line 41 is:
>>>
>>>  [ settles ]
>>>  ; OW    funct   doh     dhh
>>>  1       1       0.1     0.16333
>>>
>>>
>>>
>>> and i am using em.mdp file:
>>> ;
>>> ;       User spoel (236)
>>> ;       Wed Nov  3 17:12:44 1993
>>> ;       Input file
>>> ;
>>> cpp                 =  /lib/cpp
>>> define              =  -DFLEX_SPC
>>> constraints         =  none
>>> integrator          =  steep
>>> nsteps              =  100
>>> ;
>>> ;       Energy minimizing stuff
>>> ;
>>> emtol               =  2000
>>> emstep              =  0.01
>>>
>>> nstcomm             =  1
>>> ns_type             =  grid
>>> rlist               =  1
>>> rcoulomb            =  1.0
>>> rvdw                =  1.0
>>> Tcoupl              =  no
>>> Pcoupl              =  no
>>> gen_vel             =  no
>>>
>>> I tried the earlier post suggestion: that "include spc.itp " line
>>> must be
>>> before the "[molecule] section", but still gives the same error as:
>>>
>>> Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line
>>> 41 ]:
>>>               Atom index (1) in settles out of bounds (1-0)
>>>
>>> Thanks and regards
>>> -Alaguraj.V
>>>
>>>
>>> ALAGURAJ VELUCHAMY
>>> c/o Dr.S.KRISHNASWAMY,
>>> CENTRE OF EXCELLENCE IN BIOINFORMATICS,
>>> MADURAI KAMARAJ UNIVERSITY,
>>> MADURAI, TN.
>>> Ph:09486148690
>>>
>>>
>>> __________________________________________________
>>> Never miss an email again!
>>> Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out.
>>
>>
>>
>> ----------------------
>> TJ Piggot
>> t.piggot at bristol.ac.uk
>> University of Bristol, UK.
>>
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>
> _______________________________________________
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,	75124 Uppsala, Sweden
> phone:	+46 18 471 4537		fax: +46 18 511 755
> erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys
>
>
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.