[gmx-users] About pdb2gmx for cyclic pepetide
Mark.Abraham at anu.edu.au
Sat Sep 15 06:19:01 CEST 2012
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
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
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.
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