[gmx-users] About pdb2gmx and cyclic peptides

Ivan Gladich igladich at sissa.it
Thu Jun 26 15:05:30 CEST 2014

Thank you Justin!
Now I am going to  try


On 06/26/2014 01:49 PM, Justin Lemkul wrote:
> On 6/26/14, 6:21 AM, Ivan Gladich wrote:
>> Dear all,
>>     I am trying to build a cyclic peptide of 12 aminoacids using 
>> pdb2gmx.
>> Searching on the web I found that is not very straightforward without 
>> editing
>> the topology and the .gro file
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html 
> No need to go all the way back to 2012; this issue was discussed at 
> length just last week :)
>> The problem is that I have thousand of structures and so I need to do it
>> iteratively.
>> I am wondering if in the newer versions of gromacs the problem has been
>> addressed and solved.
> pdb2gmx was not designed with cyclic peptides in mind, but it can be 
> made to work.  If you create an entry in specbond.dat to link the 
> N-terminal N and C-terminal C, while selecting "None" for the 
> respective termini (and using -missing to override the "dangling 
> bonds" warning), then it should work, assuming the following: (1) you 
> are not using an AMBER force field, because they use fixed N- and 
> C-terminal residues that cannot be modified and (2) you have all atoms 
> (including H) built onto the starting structure (because -missing 
> creates all sorts of problems, and is used here only as a complete 
> workaround).
> Whether or not that's feasible for you to do for thousands of peptides 
> (since N- and C-terminal residue names have to be set in specbond.dat, 
> and since you need to have fully protonated structures as input) is up 
> to you.
> -Justin

Ivan Gladich, Ph.D.
Research Assistant
International School for Advanced Studies (SISSA)
Via Bonomea 265, I-34136, Trieste,

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e-mail: igladich at sissa.it
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