Dear all,
Willing to solvate a system which has been running in production run for something like 100 ns, I got stuck by reading the pdb file in tleap:
Created a new atom named: C165 within residue: .R<0 1>
The strange issue here is that the pdb itself was generated from the output of amber, and the frcmod file did its job during the previous simulations. Of course, it is a format problem, but how can this be solved?
Using antechamber is not an option since the system is very large and the pdb does contain e.g. DNA-strands. Besides, I have already an .frcmod file which was used in the not-solvated calculation.
For clearity, let me give you the different steps of my work:
-->
The pdb I started from is the final structure of a previous calculation, and reads like
ATOM 233 7C16 0 1 171.290 58.160 51.330 0.00 0.00
and the commands after "tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB" were
gaff = loadamberparams gaff.dat
loadamberparams test.frcmod
This file test.frcmod does contain all the parameters which were not available for the system I use. It reads like
ANGLE
cd-cc-ss 63.600 110.127
cc-cc-ss 63.800 120.781
...
--
Thanks for your help!
Bye,
Stefan
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Received on Wed Jan 23 2013 - 10:30:03 PST
