[gmx-users] About pdb2gmx for cyclic pepetide

[Mark Abraham]

On 15/09/2012 1:37 PM, vidhya sankar wrote:
> Dear Justin  and other Gromacs users ,
>                      Thank you for your previous reply
>             Again i Have tried  the option -missing when i use pdb2gmx tool i have got errror as follows
> My command is
>
> ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -p 2KDQ.top  -missing -ignh -ter
>
>
>
> There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
>
>   I went through a Mailing Archive Yet no body explain the proper Topology construction for cyclic peptide

http://gromacs.5086.n6.nabble.com/cyclic-peptides-tp4414209p4414219.html 
took me 5 minutes to find and looks like a good approach.

Rephrasing and adding detail, if you want a cyclic connection between 
your first and last residue, denoted FXXXXL
1) Take your initial coordinate file, make a copy and in it make a copy 
of the first residue and place it after the last residue, taking care to 
obey the format of the file you're using, and update things like atom 
counts and atom and residue indices. The coordinates of the copied atoms 
don't matter. Now you have a coordinate file for FXXXXLF.
2) Process that with pdb2gmx using -ter and choosing "none". This has 
built a linear topology for FXXXXLF, with a correct L-to-F link for you 
to use as a template for making a cyclic FXXXXL.
3) Make a copy of that .top file, and observe that the numbers of 
corresponding atoms in the two F residues are separated by the same 
amount of atoms. Record that amount, call it x.
4) In the [bonds], etc. sections, identify all the interactions between 
L and F, and subtract x from the number of the in F, so that these 
interactions now refer to the initial F. This makes the cyclic link 
correctly, because you've used a correct L-to-F link as a template.
5) Remove all the remaining references to the final F from [atoms], and 
also from [bonds], etc. (which will only be internal bonds, because 
you've changed all the other ones)
6) Remove any surplus hydrogen atoms attached to the N-terminus of the 
initial F.
7) Now your initial coordinate file and this edited .top file should be 
good to use with grompp to generate a cyclic .tpr. Pay attention to the 
errors and warnings it gives and act appropriately. Recall that the atom 
ordering must match between the coordinate file and .top file you are 
using, but this construction ensures this.

If you want to use the generated posre.itp file, you'll need to make 
corresponding adjustments to it.

> It Discussed about Manual editing of topology But in my case it is headache
>
> Because my cyclic peptide contains large number of atom

The number of atoms in your peptide doesn't matter for editing the 
topology to make a cyclic connection.

> How to solve this problem without manual editing

You'll have to, if you can't make 
http://www.gromacs.org/Documentation/File_Formats/specbond.dat work for you.

You can file a feature request on the GROMACS Redmine site for 
constructing cyclic peptides with pdb2gmx, but it will not get dealt 
with any time soon. Feedback on the above kind of procedure here or 
there would be welcome.

Mark