From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Mar 02 2018 - 14:29:26 CST
It's been a while since I looked at an AMBER topology (they have this in
RTF format now?) - but I recall that OS is an ester oxygen and thus should
never be bound to a hydrogen (HO). Maybe there is an incorrect atom-type or
bond somewhere in the RTF?
Keep in mind also that "patch" commands in psfgen generally do NOT result
in the correct atom connectivity. You should probably call "regenerate
angles dihedrals" before writing your PSF.
On Fri, Mar 2, 2018 at 2:55 PM, Ashutosh Shandilya <scfbioiitd_at_gmail.com>
> Dear NAMD users
> I have made psf and pdb file and ran the simulation without error but when
> I introduce a break in the chain it gives me following error. Attached are
> two input files (1.inp and 1_new.inp) the only difference between two is
> one has a break in the chain with same coordinates. Any insight regarding
> this error would be helpful.
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