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

[martinez]

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