Unnatural Bond lengths

From: Vinit Rege (vrege_at_asu.edu)
Date: Sat Nov 11 2006 - 01:56:35 CST

 Hello all,

I am having troubles with making PSF of some PDBs which have a residuename
LIP unrecognised by CHARMM... but I was successful overriding that problem
and get it done with POPC...(mapping, as suggested)... but when I load new
PDB and PSF in VMD, I get some unnatural bonds for:

Pair 1 - H11 and C11
Pair 2 - H11R and C211

...I dont have a clue of why this is happening...when I view it in VMD, I
can see elongated bonds (Hydrogen atoms placed faar away from Carbons
mentioned) ... I can manually translate atoms (Hydrogens) close to Carbons
in VMD, but since I have total of around 200 lipids in my structure, doing
this for every one of it would be impossible...

Can somebody enlighten me of why those unnatural bonds are created ?


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