AMBER Archive (2009)

Subject: Re: [AMBER] Atom type error

From: Vikas Sharma (
Date: Sun Apr 19 2009 - 11:50:28 CDT

Dear Nichlous
Dear Carlos
Thanks for the reply..but its the problem with the protein...since i prepared the protein in sybyl it has deprotonated the -COOh and protonated the -NH2...i'l try to change the atom types..if u have any idea please let me know

From: nicholus bhattacharjee <>
To: AMBER Mailing List <>
Sent: Sunday, 19 April, 2009 4:25:37 PM
Subject: Re: [AMBER] Atom type error

Dear Vikash,
                    Its seems to me that you have not neutralized your
molecule m. It is showing unperturbed charge of 9.000000. So after loading
your pdb file run the following command

addions m Cl- 0

Hopefully it will work.

On Sun, Apr 19, 2009 at 5:48 AM, Vikas Sharma <>wrote:

> Dear All,
> I have done molecular docking of a few ligands on a protein...nw i wish to
> calculate binding free energy of those ligands using MM PBSA
> I performed the following steps:
>  source leaprc.ff03
>  m = loadpdb A.pdb
>  saveamberparm m A.prmtop A.inpcrd      then the output was
>  warning:The unperturbed charge ofthe unit:9.000000 is not zero
>  Fatal: Atom .R<CXL 232>.A<C 1> doesnt have a type
>  Fatal: Atom .R<CXL 232>.A<O2 2> doesnt have a type
>  Fatal: Atom .R<CXL 232>.A<O1 3> doesnt have a type
>  Fatal: Atom .R<AMN 233>.A<N 1> doesnt have a type
> Failed to generate parameters
> What should i do now??
> i performed molecular docking using Sybyl..
> i checked in sybyl and got the following information    1. N-terminal
> configuration (charged=AMN; neutral=AMI).
>        2. C-terminal configuration (charged=CXL; netural=CXC).
> this means that while protein preparation C-terminal and N-terminal have
> become charged
> Ihave the same protein with ligand on which i have perform the steps as
> mentioned in the tutorial (like minimizing,heating,equilibrating)
> Please helpppppppp....
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Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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