Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 21 Jul 2010 11:10:56 -0400

Hello,

A slight modification to Professor Case's statement. In this case, you made an off library, so he residue name in DXQ.lib or whatever you called it must be the same as that residue's name in the pdb you're loading. It looks like it's called LIG in the pdb, but not in the off file. You can just change the residue name in the pdb to match the library for each atom in that residue.

Hope this helps,
Jason

--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
On Jul 21, 2010, at 9:09 AM, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Jul 21, 2010, kamlesh sahu wrote:
>> 
>> I am using amber 10 to simulate small molecules (modified a little as
>> compared to original pdb structure). First I used antechamber to fit ligand
>> parameters and then I used tleap to generate library in this way -
>> ~/src/Xtruct/trunk/amber_10_install/bin/antechamber -i DXQ-11_h.pdb -fi pdb
>> -o DXQ-11.mol2 -fo mol2 -c bcc -s 2 -j 5 -nc +2
>> 
>> 
>> It gives error messages -
>> 
>> FATAL:  Atom .R<LIG 1184>.A<CAA 1> does not have a type.
> 
> This generally means that atom or residue names in the pdb file don't match
> those in the DXQ-11.mol2 file you created above.  You have to make them
> exactly match, and the names are case-sensitive.
> 
> Also, study the leap.log file carefully: there should be other messages
> pointing out the problem, especially if my diagnosis is correct.
> 
> ....dac
> 
> 
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Received on Wed Jul 21 2010 - 08:30:05 PDT