[gmx-users] Incorrect .top file numbering

Ashutosh Jogalekar ajogale at emory.edu
Mon Mar 6 22:09:11 CET 2006

It's just a regular peptide with the sequence KLVFFAE
One of the Phenylalanines (the first one from the left is replaced  
with phenylglycine. The ends are capped with acetyl and NH2 groups. I  
could parametrize the acetyl, because that needed me to put in just  
one dihedral. There are 7 strands of the peptide which form a sheet.  
Seven such sheets in turn are stacked on top of each other. This is  
the system I want to do MD on. I did use -merge in the pdb2gmx  

On Mar 6, 2006, at 1:37 PM, Mark Abraham wrote:

> Ashutosh Jogalekar wrote:
>> I am trying to do an MD on a peptide with an unnatural amino acid   
>> residue. When I convert the pdb to the gro file and generate  
>> the .top  file, the amino acid residues are numbered incorrectly.  
>> The first  three are numbered ok from 1-3. But after the third  
>> one, the next one  is numbered 5 instead of 4, and after that, all  
>> the others are  numbered successively. Why is this happening?
> We needed more information. Where is the unnatural amino acid? What  
> does your pdb file have in the region 3-5?
> Mark
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