I have used "pdb4amber -i rnacomplex.pdb -o new.pdb --nohyd --dry" this
command to remove hydrogens. I got a notice "gap of 5.280009 A between
VAL_162 and PHE_163
You MUST (!!!) insert a TER record between the residues listed above and
consider to introduce caps (ACE and NME) at the dangling N- and
C-terminals". So, I have added TER statement in the PDB file between VAL
162 and PHE 163 residues now I can able to generate prmtop and inpcrd
files. can you please tell me why it is asking to add TER statement and
what it is doing???
On Fri, Mar 11, 2016 at 7:19 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 11 2016 - 22:30:04 PST
