Dear All,
I am using packmol-memgen to pack into a membrane protein with bound ligand using the command below on pdb4amber cleaned pdb file ((
https://pastebin.com/raw/ZNgBAqzA))
$AMBERHOME/bin/packmol-memgen --pdb placed.clean.pdb --lipids POPC:POPE --ratio 2:1 --preoriented --salt --salt_c K+ --saltcon 0.15 --notprotonate --nottrim --keepligs --ligand_param FMA.frcmod:fma.lib --gaff2 --parametrize --ffwat opc --ffprot ff19SB --fflip lipid21
All goes fine until tLeap runs saveAmberParam command on the packmol-edited .pdb file (
https://pastebin.com/raw/VnXXjPad) when the error appear:
> saveAmberParm SYS bilayer_placed.clean_lipid.top bilayer_placed.clean_lipid.crd
Checking Unit.
/opt/exp_soft/local/skylake/amber/22/bin/teLeap: Warning!
There is a bond of 3.161 angstroms between CA and C atoms:
------- .R<SER 14>.A<CA 3> and .R<SER 14>.A<C 10>
FATAL: Atom .R<LYS 233>.A<OXT 23> does not have a type.
/opt/exp_soft/local/skylake/amber/22/bin/teLeap: Fatal Error!
Failed to generate parameters
Exiting LEaP: Errors = 1; Warnings = 664; Notes = 1.
I wonder what could be the reason (full log: https://pastebin.com/raw/MhEaL4tr)
Thanks in advance
–
Maciej Spiegel, MPharm PhD
assistant professor
.GitHub <
https://farmaceut.github.io/>
Department of Organic Chemistry and Pharmaceutical Technology,
Faculty of Pharmacy, Wroclaw Medical University
Borowska 211A, 50-556 Wroclaw, Poland
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Received on Mon Sep 23 2024 - 01:30:02 PDT
