AMBER Archive (2009)

Subject: Re: [AMBER] Atom type error

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Sun Apr 19 2009 - 11:49:53 CDT

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: Carlos Simmerling <carlos.simmerling_at_gmail.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Sunday, 19 April, 2009 4:36:07 PM
Subject: Re: [AMBER] Atom type error

I don't think that's it- the charge has a warning, but that is not
fatal. the fatal part is that some of the atoms don't have atom types
defined, so there is no way to apply bonds, etc. you have loaded ff03,
but it probably doesn't have parameters for your ligands. you will
need to learn to use antechamber- check out the tutorials on the amber
web page, they should get you started. also make sure you are already
familiar with using amber and MD before you start to work on new
molecules (not proteins or nucleic acids or other standard residues).
they are things that can go wrong and you likely need experience to
recognize them.

On Sun, Apr 19, 2009 at 6:55 AM, nicholus bhattacharjee
<nicholusbhattacharjee_at_gmail.com> wrote:
> 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 <vs_vikassharma_at_yahoo.co.in>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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