[gmx-users] simulation of infinite chains

[sang eun jee]

Dear gromacs users

Previously, I simulated collagen triple helix chains,  (GLY-PRO-HYP)n using
Amber99sb-ILDN forcefield. When I processed pdb structures with pdb2gmx, I
only obtained GLY in the N termini properly, and HYP was not processed(it
was treated like HYP, not terminal HYP)  since there was no HYP library
describing C termini. Therefore, I added CHYP data in library and
everything was fine.

Now I am trying to simulate infinite collagen triple chains, (GLY-PRO-HYP)n
where GLY in N-terminus is connected to the HYP in C-terminus through the
periodic boundary condition. So, I would like to process structures with
pdb2gmx and wanted to treat NGLY and CHYP in termini as a GLY and HYP.  So
I removed CHYP library I added before, and removed NGLY library too.
Without NGLY library, However, pdb2gmx does not work well and says there is
dangling bond so investigate *.rtp or *.tdb.  Without CHYP library, pdb2gmx
worked well and just processed CHYP like HYP, Does anyone know why this
error occurs in case of N-termini?

Thanks for you advice in advance.

Sincerely,

Sangeun Jee



-- 
Post Doctoral Researcher
School of Materials Science and Engineering
Georgia Institute of Technology