Re: [AMBER] antechamber warning

From: Saman Yousuf ali <>
Date: Thu, 23 Feb 2017 04:08:12 +0000 (UTC)

Dear Scott,I have attached orignal co-crystal pdb .chimera edited pdb and output of antechamber here. I used following antechamber command to gernerate prepin and frcmod files.
antechamber -fi pdb -i LYA-chimera-edtd.pdb -fo prepc -o LYA.prepin -c bcc -s 2 -nc 0 -m 1parmchk -i LYA.prepin -f prepc -o LYA.frcmod
Kindly check and identify any mistake.
Thanks Best Regards, Saman Yousuf AliJunior Research Fellow,

    On Thursday, February 23, 2017 12:23 AM, Scott Brozell <> wrote:


If you followed the general advice and are having issues then we need to
see the details.  Please send both the input and outputs to and from both
chimera and antechamber.


On Wed, Feb 22, 2017 at 08:11:57AM +0000, Saman Yousuf ali wrote:
> Dear Scott,Thank for your response, I visualized prmtop and inpcrd file ligand-protein complex structure is perfect with all hydrogen atom on correct position in waterbox. Actually in orignal pdb atom typing of two nitrogen of co-cystallized ligand were disturbed. When I add hydrogen via chimera then hydrogen was added to wrong position. Then I change Npl atom type to N2 for nitrogen N16 and N2 to Npl for N18 using setattr command. After that I again add hydrogen using structure editing option and run antechamber for preparing prepin and frcmod file. Please suggest me any other method for changing atom type to avoid this waring.Thanks
>    On Wednesday, February 22, 2017 12:11 PM, Scott Brozell <> wrote:
>  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 Wed Feb 22 2017 - 20:30:03 PST
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