Dear Amber users !
I am using packmol-memgen for the preparation of GPCR system in water with
following parameters
/amber/22b/bin/packmol-memgen --pdb gpcr.pdb --lipids POPC:TOCL --salt_c
Na+ --ffprot ff14SB --fflip lipid21 --ratio 90:10 --keepligs --ligand_param
lig.frcmod:lig.lib --parametrize --minimize
Briefly, it produces bilayer with the correctly inserted protein but at
the final step of parametrization I got the following error:
> SYS = loadpdb cli_clean.pdb
Loading PDB file: ./cli_clean.pdb
Matching PDB residue names to LEaP variables.
Mapped residue CYX, term: Terminal/beginning, seq. number: 0 to: NCYX.
Mapped residue LYS, term: Terminal/last, seq. number: 307 to: CLYS.
Bond: maximum coordination exceeded on .R<WAT 19447>.A<H2 3>
Bond: Maximum coordination exceeded on .R<WAT 19877>.A<H1 2>
-- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<WAT 19447>.A<H2 3> .R<WAT 19877>.A<H1 2>
indicating that there is some problem with water in the prepared system
How could this issue be solved ?
Many thanks in advance
Enrico
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 23 2024 - 02:00:02 PDT
