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
<[EMAIL PROTECTED]> 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
<[EMAIL PROTECTED]> 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
[EMAIL PROTECTED]
University of Bristol, UK.
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
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
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
