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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