[gmx-users] Problems with pdb2gmx simulating a iron-sulfur cluster

[Tsjerk Wassenaar]

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 <nicolas.martinez at ibs.fr> 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
>
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-- 
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