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

[Mark Abraham]

On 25/08/2011 3:10 AM, Pablo Englebienne wrote:
> 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:
>
> -NH2-CH2-[CH2-O-CH2]n-CH2-C(=O)-
>
> The system looks like this:
>
> N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ-C-(PEG)-N
>
> So:
> * the C-terminus of a PEG linker is attached to the N terminus of the 
> peptide
> * the terminal Lys on the peptide is attached to the C-terminus of a 
> PEG linker
>
> 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:
>
> N-(peptide1)-C-N-(PEG)-C-N-(peptide2)-Lys(C-ter)-NZ-C-(PEG)-N-C-(peptide3)-N 
>
>
> 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- || 
> -C-(PEG)-N-C-(peptide3)-N
>
> 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]
> n
>
> 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:
>                   PEA118
>                   CG1125
>   LYSS27   NZ198   2.762

That's a long bond. Does your reference length in specbond.dat suit it? 
IIRC there should be some evidence in the output of the special bond 
being formed if it actually is. If not, your symptoms are probably related.

Oh, and well done for constructing a good question. You would likely not 
have gotten anywhere giving less detail :)

Mark

> Select start terminus type for ARG-1
>  0: NH3+
>  1: NH2
>  2: None
> 0
> Start terminus ARG-1: NH3+
> Select end terminus type for LYSS-27
>  0: COO-
>  1: COOH
>  2: None
> 0
> 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
> 0
> Start terminus GLU-28: NH3+
> Select end terminus type for PEA-47
>  0: COO-
>  1: COOH
>  2: None
> 2
> 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!
>