On Fri, Mar 11, 2016, Sreemol G wrote:
> Actually i have tried but i'm getting errors when i try to save my topology
> and coordinate files.I have used the forcefield "leaprc.ff14SB" when i
> loaded pdb i got the message and when i tried to save the topology file and
> coordinate file i'm getting following error
> Created a new atom named: HT1 within residue: .R<NGLY 18>
> Created a new atom named: HT2 within residue: .R<NGLY 18>
> Created a new atom named: HT3 within residue: .R<NGLY 18>
> Created a new atom named: HN within residue: .R<ARG 19>
...etc
To expand on what Vlad said, your input PDB has very non-standard atom names
(where did it come from?). Simplest approach (which Amber users should use
much more often!) is to use pdb4amber with the "--nohyd" option to remove
hydrogens. See the manual, or just type "pdb4amber --help" to get more info.
...dac
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Received on Fri Mar 11 2016 - 06:00:10 PST
