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

[Yang Ye]

You need to put the atom types defined in ffamber under [ atoms ] as 
replacement of original

     1  amber99_54   1  SOL     OW      1      -0.82  15.99940
     2  amber99_55   1  SOL    HW1      1       0.41   1.00800
     3  amber99_55   1  SOL    HW2      1       0.41   1.00800

It is good to embrace it with some C preprocessor so as to make SPC 
still works for other force field,

#ifdef (_FF_AMBER99)
     1  amber99_54   1  SOL     OW      1      -0.82  15.99940
     2  amber99_55   1  SOL    HW1      1       0.41   1.00800
     3  amber99_55   1  SOL    HW2      1       0.41   1.00800
#else
     1  OW  1    SOL     OW      1      -0.82
     2  HW  1    SOL    HW1      1       0.41
     3  HW  1    SOL    HW2      1       0.41
#endif

TJ Piggot wrote:
> 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
>>
>>
>> __________________________________________________
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>
>
>
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>
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