Hello,
I'm actually trying to build a water-urea mixture box with different urea
concentrations.
I'm generating .prm and .rst files in tleap using the following input:
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams frcmod.urea
loadamberparams frcmod.ionsjc_tip3p
loadoff urea_h.lib
URE = loadpdb test.pdb
set URE box { 22.336 22.336 23.445 }
savepdb URE test_2.pdb
saveamberparm URE ure.prm ure.rst
The urea_h.lib (-> urea_h) is attached. I did this myself by loading one
urea molecule into tleap and saving it as .lib file.
The test.pdb file is generated by a self written program.
Everything works fine, however, when saving the .prm and .rst files, I get
following warnings:
Warning: Unbonded Hydrogen atom H1 in URE.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
Warning: Unbonded Hydrogen atom H2 in URE.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
(I get this warning for all of the URE molecules)
So it seems like there are no bonds. When visualizing the output pdb file
in vmd, everything seems to be ok. However, when I try to start a
minimization run, it doesn't even start. I used the min.in input with other
systems, where it did work.
So, I don't see where I made mistakes (in tleap perhaps ?) and I hope, that
you can help me.
(I'm using the Amber18 package.)
Thank you
Nora
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- application/octet-stream attachment: urea_h
- application/x-aportisdoc attachment: test.pdb
Received on Tue Jun 11 2019 - 07:30:02 PDT
