On Fri, Apr 29, 2016, Anna Cebrian Prats wrote:
>
> I try to use the prep and frcmod get it from data base ( added in this email), for the group heme (UNIT HEM)
>
> For atom: .R<HEM 556>.A<NA 2> Could not find vdW (or other) parameters for type: NP
Arrgh...somehow the frcmod.hemall file on the web site is out of date.
Try the one attached here...just has two additional lines at the bottom,
defining vdW parameters for NP and NO.
Thanks for being patient, and for pointing this out. I'll get the files fixed
on the web database.
Here is a leap.in file (annotated slightly) that I recently used to construct
a model that has two Mb-like proteins:
source leaprc.ff14SB
source leaprc.gaff # need this for my ligand
loadAmberPrep heme_all.in
loadAmberParams frcmod.hemall # use the version attached in this email
CMO = loadMol2 cmo.mol2 # my ligand, which is CO
SO4 = loadMol2 SO4_ipq_spce.mol2 # sulfate ions also in the simujlations
loadAmberParams SO4_ipq_spce.frcmod
loadAmberParams frcmod.spce # I decided to use SPC/E water here
loadAmberParams frcmod.ionsjc_spce
WAT=SPC
HOH=SPC
x = loadpdb 1bzr_ucnawat.pdb # loading the pdb file
bond x.93.NE2 x.154.FE # add the bond from the His to Fe of the hem
bond x.250.NE2 x.311.FE
bond x.155.C x.154.FE # add bond between Fe and the CO liagnd
bond x.312.C x.311.FE
set x box {34.910 31.040 64.730} # I already had waters, you might do
# something like solvateOct here
saveamberparm x 1bzr_uc_wet.parm7 1bzr_uc_wet.rst7
savepdb x 1bzr_uc_wet.pdb
quit
...hope this helps...dac
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Received on Fri Apr 29 2016 - 09:30:06 PDT
