[gmx-users] Multiple peptides
feenstra at chem.vu.nl
Thu Dec 11 09:23:08 CET 2003
> On Tue, 2003-12-09 at 08:48, Aswin Narain wrote:
>>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
>>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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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