Re: [AMBER] antechamber warning

From: Scott Brozell <>
Date: Wed, 22 Feb 2017 02:11:36 -0500

On Wed, Feb 22, 2017 at 06:18:13AM +0000, Saman Yousuf ali wrote:
> Dear All,I got following warning while running antechamber for ligand preparation.
> saman.mcg18:/data-store/ds_Working_sya/modelling-t.b.ptr1/2X9G/LY1/test> ./antec
> hamber
> Running: /usr/local/amber14/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
> Running: /usr/local/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC
> .AC -p gaff
> Total number of electrons: 224; net charge: 0
> Running: /usr/local/amber14/bin/sqm -O -i -o sqm.out
> Running: /usr/local/amber14/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMB
> ER_AM1BCC.AC -f ac -p /usr/local/amber14/dat/antechamber/BCCPARM.DAT -s 2 -j 1
> Running: /usr/local/amber14/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -
> Running: /usr/local/amber14/bin/prepgen -i ANTECHAMBER_PREP.AC -f car -o LY1.pre
> pin -rn "LY1" -rf molecule.res
> Warning: ATOM N16 has unfilled valence, assuming the linked atom name (in other
> residue) is "M"
> ???????? change "M" to "-M" if ATOM N16 is linked to the immediate previous resi
> due
> ???????? change "M" to "+M" if ATOM N16 is linked to the immediate after residue.
> I have added hydrogen in ligand using structure editing command chimera, before adding hydrogen I have modify atom typing of nitrogen atom and oxygen atoms of carbonyl carbon using setattr command of chimera. Then I checked coordinates of atoms and matched with pdb file coordinates of ligand atoms. Prepin and frcmod file are generated perfectly with out any change in coordinates. Should I safely ignore above error or it may cause trouble during md? Please suggests your views.

Usually this error is caused by an incomplete or erroneous input structure.
The general advice is to double check your work: Verify that chimera did
what you intended, visualize your final structure, check the stoichiometry
and total charge, etc.


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Received on Tue Feb 21 2017 - 23:30:02 PST
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