[gmx-users] Difficulty building a topology for a synthetic branched PEG-peptide molecule

Pablo Englebienne p.englebienne at tue.nl
Wed Aug 24 19:10:31 CEST 2011

Hi all,

I am trying to build a topology for a synthetic molecule that consists 
of peptides connected by oligoethyleneglycol (I'll call it PEG) linkers 
terminated with an amine and a carboxylic acid:


The system looks like this:


* the C-terminus of a PEG linker is attached to the N terminus of the 
* the terminal Lys on the peptide is attached to the C-terminus of a PEG 

I was able to successfully build a topology for this molecule by:
* defining appropriate residues (for the PEG chains and the Lys with a 
PEG attached on the NZ) in a local copy of the forcefield file, adding 
the residues' topologies to aminoacids.rtp
* using the specbond.dat file to define the bond between the NZ in the 
Lys and the PEG linker
* adding the residues to residuetypes.dat with a "Protein" type
* calling pdb2gmx with the -ter option to assign the protonation states

Now, I need to extend the topology to a molecule like this one:


The difficulty with this molecule is that it has 2 N-termini and a 
single C-terminus (in the Lys with the PEG attached to the NZ 
sidechain). pdb2gmx recognizes the whole molecule as a peptide, but 
treats the last residue as a C-terminus, when it actually is an N-terminus.

I found in the description for specbond.dat 
(http://www.gromacs.org/Documentation/File_Formats/specbond.dat) that 
for a branched peptide the "-chainsep" option of pdb2gmx can be used, so 
I started to work on that. I split the molecules in 2 chains like this:

N-(peptide1)-C-N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ- || 

I reversed the order of the residues in the second chain, so that the 
residues are in N-to-C order. With this, pdb2gmx recognizes the proper 
termini when called as:

$ pdb2gmx -f substrate_edited-reversed.pdb -ter -chainsep interactive

I tried setting the protonation of the termini as charged for the "real" 
termini and None for the artificial one (the one that should be handled 
by specbond.dat), but I get an error message:

---[pdb2gmx output]---
Splitting PDB chains based on TER records or changing chain id.
Merge chain ending with residue LYSS27 (chain id ' ', atom 71 NZ) with
chain starting with residue GLU28 (chain id 'p', atom 308 OE2)? [n/y]

Merged 1 chains into one molecule definition

There are 2 chains and 0 blocks of water and 47 residues with 303 atoms

   chain  #res #atoms
   1 ' '    27    198
   2 'p'    17    105
Identified residue ARG1 as a starting terminus.
Identified residue LYSS27 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   LYSS27   NZ198   2.762
Select start terminus type for ARG-1
  0: NH3+
  1: NH2
  2: None
Start terminus ARG-1: NH3+
Select end terminus type for LYSS-27
  0: COO-
  1: COOH
  2: None
End terminus LYSS-27: COO-
Identified residue GLU28 as a starting terminus.
Identified residue PEA47 as a ending terminus.
9 out of 9 lines of specbond.dat converted successfully
Select start terminus type for GLU-28
  0: NH3+
  1: NH2
  2: None
Start terminus GLU-28: NH3+
Select end terminus type for PEA-47
  0: COO-
  1: COOH
  2: None
End terminus PEA-47: None
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2top.c, line: 1035

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a 
proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---[pdb2gmx output]---

I think that the problem might stem from the fact that the C-terminus in 
the second chain is not a real peptide; I changed residuetypes.dat to 
have the PEG residues as "Other", which causes pdb2gmx to recognize the 
last aminoacid as a C-terminus, but treating it as "None" yields the 
same error. Unfortunately, there is nothing about this error in 
http://www.gromacs.org/Documentation/Errors .

Any suggestions on how to make this work will be greatly appreciated!


Pablo Englebienne, PhD
Dept. of Biomedical Engineering
Dept. of Chemistry and Chemical Engineering
Institute for Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349

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