[gmx-users] grompp erro

Albert mailmd2011 at gmail.com
Sun Jan 19 21:04:26 CET 2014

thanks a lot for kind reply.

Now I noticed that this comes from the terminal residues after I further 
confirmed and repeated it again instead of protonated residues.

I run: pdb2gmx -f mae.pdb -ignh -o test.pdb -ter

Select start terminus type for THR-19
  0: NH3+
  1: NH2
  2: 5TER
  3: None
Start terminus THR-19: NH2
Select end terminus type for CYS-322
  0: COO-
  1: COOH
  2: CT2
  3: 3TER
  4: None

if I don't add option "-ter", this error doesn't happen.


On 01/19/2014 05:41 PM, Justin Lemkul wrote:
> All of this is critical information that you left out of your original 
> post, hence my assumption that your issue could be easily solved.  
> When reporting a problem, please be as specific as possible!  If there 
> is a problem with our latest parameters, we need to fix that, but I 
> don't yet have enough information to tell you what's wrong.  grompp 
> did, however, give you what you need to figure it out.  The fatal 
> error comes from line 23560 of the topology file.  What is on that 
> line?  What are those atoms and what are their types?
> -Justin

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