[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins
jalemkul at vt.edu
Sat Sep 22 14:11:41 CEST 2012
On 9/22/12 7:08 AM, James Starlight wrote:
> sorry I forgot to specify that I also refreshed topology for my
> protein by pdb2gmx.
> after I've created new 54a7_lipid.ff in the gromacs dir I applied
> pdb2gmx on the protein model only. Than I copied part of that new
> topology (with the parameters of protein) to old topology of the
> entirely system ( protein+lipids+water). So I have protein and spc
> water parametrised in 54a7 ff and lipids - in berger's 53a6. If new
> 54a7 ff include only updates to dihedrals should I use old cut-offs ?
You will have to determine that yourself. I use the 1.2 nm cutoffs for
53A6+Berger because I found that they produce reasonable results. I have no
such insight for 54A7.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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