Re: [AMBER] Problems adding molecule on Metal-Water system

From: David Case <>
Date: Mon, 9 Dec 2019 17:46:38 +0000

On Fri, Dec 06, 2019, Lucas Bandeira wrote:
> AddToBox -c interfaceNaOH.pdb -a NaOHGlycerol/AmberGlyceroxide.pdb -na 10
>-P 5178 -o interfaceGlycerol.pdb -RW 2.5 -RP 2.5 -G 0.1 -V

Here's what I get with your input files:

dirac% AddToBox -c interfaceNaOH.pdb -a AmberGlyceroxide.pdb -na 10 -P 5178 -o interfaceGlycerol.pdb -RW 2.5 -RP 2.5 -G 0.1 -V
pdbRead >> Error. PDB file must contain CRYST1 card!

Is it possible that the "interfaceNaOH.pdb" file you sent is not the one
you actually used? (I don't see any CRYST1 card. Note that this card
needs to have the unit cell parameters, not just the letters "CRYST1").


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Received on Mon Dec 09 2019 - 10:00:01 PST
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