Hi Nicolas,
I don't see any warnings concerning bonds, so it seems these are
handled correctly. Check the atom numbers and types of the angles (and
dihedrals) this concerns and try to find out why it doesn't work the
way you want it to ( = homework).
Best,
Tsjerk
On 4/23/07, martinez <[EMAIL PROTECTED]> wrote:
Hi Martinez,
pdb2gmx doesn't do that for you. grompp does. With the specbond.dat
you let pdb2gmx find the bonds and list them in the topology. When
running grompp, it will apply a default bond/angle/dihedral type for
bonds/angles/dihedrals listed, but for which no parameters are given,
based on the [ default_*s ]. You can check whether grompp did a good
job by using the -po option, which should contain the full topology as
it is constructed for and present inside the .tpr file. This means
without any #defines, #includes, etc..., everything filled in
explicitly. Sorry I wasn't clear on this point.
Best,
Tsjerk
Thank you Tsjerk
I tried to run grompp with the topology file as you told me but grommp
gives me a message error because this file is incomplete. this is what
it tells me:
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
WARNING 1 [file "topol.top", line 9586]:
No default G96Angle types, using zeroes
WARNING 2 [file "topol.top", line 9617]:
No default G96Angle types, using zeroes
WARNING 3 [file "topol.top", line 10860]:
No default G96Angle types, using zeroes
WARNING 4 [file "topol.top", line 11281]:
No default G96Angle types, using zeroes
WARNING 5 [file "topol.top", line 11812]:
No default G96Angle types, using zeroes
WARNING 6 [file "topol.top", line 11858]:
No default G96Angle types, using zeroes
WARNING 7 [file "topol.top", line 12247]:
No default G96Angle types, using zeroes
WARNING 8 [file "topol.top", line 12334]:
No default G96Angle types, using zeroes
WARNING 9 [file "topol.top", line 12469]:
No default G96Angle types, using zeroes
WARNING 10 [file "topol.top", line 12752]:
No default G96Angle types, using zeroes
Cleaning up temporary file gromppqJFYTB
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: fatal.c, line: 416
Fatal error:
Too many warnings, grompp terminated
----------------------------------------
...
Why doesn't he give the bonds/angles/dihedrals types the default values?
Thank you for your help.
Nicolas
_______________________________________________
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
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
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
