Re: [AMBER] Problems during solvation of molecule from Protein Data Bank

From: The Cromicus Productions <>
Date: Mon, 12 Dec 2016 16:53:04 -0500

Sorry, got sent.
HETATM 489 N1 SPM A 26 15.754 28.140 88.337 1.00 17.38
and that I need to load a new library, but which one?
This is my code

source leaprc.ff14SB

source leaprc.water.tip3p

loadAmberParams frcmod.ionsjc_tip3p

dna1= loadpdb "nuc.pdb"

saveAmberParm dna1 dnainvacuum.prmtop dnainvacuum.inpcrd

addions dna1 Na+ 0

saveamberparm dna1 dnaneutral.prmtop dnaneutral.inpcrd

dna2=copy dna1

solvatebox dna1 TIP3PBOX 10.0

edit dna2

saveamberparm dna2 dnainwater.prmtop dnainwater.inpcrd

On Mon, Dec 12, 2016 at 4:52 PM, The Cromicus Productions <> wrote:

> Hi everyone,
> I'm trying to solvate the molecule 1S2R in tLeap but I'm getting the
> following errors:
> FATAL: Atom .R<SPM 25>.A<N1 1> does not have a type.
> and others just like that one. I believe it is due to the atoms
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Received on Mon Dec 12 2016 - 14:00:03 PST
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