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

[Erik Marklund]

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.
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_______________________________________________
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