Dear Amber developers and users
I am attempting to use tip4pfb water model to solvate a peptide.
Initially I sourced the leaprc.protein.ff14SB file in addition to loading
solvents.lib, frcmod.tip4pfb and atomic_ions.lib files. After solvating the
peptide in FB4BOX, using the addions (or addions2) I added 2 Na+ ions
without any errors (the Na+ exists in Unit list). However, when I try to
save the prmtop and inpcrd files, I get this error (leap.log file is
attached to this E-mail):
*For atom: .R<Na+ 520>.A<Na+ 1> Could not find vdW (or other) parameters
for type: Na+*
Now, I understand that I need to source ion parameters using files such
as leaprc.water.tip4pewFB4 and frcmod.ionsjc_tip4pewFB4 for FB4BOX water
model, except that these files do not exist. Any suggestions on how I can
find these parameters would be greatly appreciated.
Best Regards
samaneh
P.S. The system is a peptide (ACE LYS NME) with overall charge state of +3
in water. The error message does not appear when I use tip3fb water model
with related force field files.
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Thu Jan 05 2017 - 10:00:02 PST
