Hello Steve,
> Setting up a complex of a number of PEG chain linked units I then run
> antechamber to obtain charges and input files.
> The MD simulation uses igb=1.
> After equilibrating to 300K I examine the MD output and the molecules show no interaction i.e. they seem to be frozen with no twisting and no vdW nor charge interactions. When running using a Dreiding force field for example in other MD packages there is a great deal of interaction. Can anyone advise what might be going wrong or would this be expected using the Gaff force field.
I used TEG as a spacer molecule parameterized like a pseudo-amino acid,
i.e. with an C- and N-terminus (Amber, gaff; DOI: 10.1021/ja107675n).
Thus, I was able to use it as a spacer or link several TEG units
together, like Francois suggested.
In our simulations, the TEG moiety was very flexible and exhibited
distinct interactions with the peptide environment.
=> There should definitely be conformational change and interaction in
your PEG unit.
Regards,
Anselm
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Received on Tue Jun 18 2013 - 06:00:03 PDT
