[gmx-users] Multiple peptides

[Anton Feenstra]

David wrote:

> On Tue, 2003-12-09 at 08:48, Aswin Narain wrote:
> 
>>Hi all
>>
>>Thanks for the prompt response. I tried giving chain
>>identifiers. Everything worked but EM didnt finish to
>>required precision (but only to machine precision).
>>The the dynamics also failed. LINCS warning turned up
>>and 1-4 interactions also showed up and the simulation
>>crashed.
>>
>>SO what to do now??
> 
> Check the structure file, see which 1-4 interaction breaks (by running
> mdrun -debug). Check for large energies.

It may be that your peptides got turned into one single chain
by pdb2gmx. That would explain the 1-4 errors. Check the output
of pdb2gmx for warnings about long bonds. Add chain identifiers
to the separate peptides so pdb2gmx can see where they end.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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