[gmx-users] Problems with pdb2gmx simulating a iron-sulfur cluster
martinez
nicolas.martinez at ibs.fr
Mon Apr 23 14:04:17 CEST 2007
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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