[gmx-users] Re: Error during executing the protein ligand tutorial

[Justin A. Lemkul]

bharat gupta wrote:
> Hi,
> 
> In addition to my last mail, I am also getting another error during the 
> minimization step. I made the changes in em_real.mdp file for my sytem 
> but its showing the error that "ource code file: readir.c, line: 1316
> 
> Fatal error:
> Group PTR not found in indexfile.
> "
> 

I'm guessing you failed to follow step 5 here:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

> also the charge on the system now is 8 .... pls help

Take another look at the screen output regarding net charge before adding ions. 
  I suspect you're missing an exponent.  But I'd echo what Mark has said - 
always provide real output directly copied from the screen, or else we're left 
to our suspicions and guesses, which ends up wasting everyone's time.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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