Thank you so much for your reply.
"parmed" and "ambpdb" helped me so much to solve my problem.
Best regards
----------------------------------------------
Sangita Kachhap
Post Doctoral FellowJerzy Haber Institute of Catalysis and Surface Chemistry
Polish Academy of Sciences
Niezapominajek 8
PL-30239 Krakow, Poland
----------------------------------------------
On Tue, May 19, 2020 at 1:43 PM David A Case <david.case.rutgers.edu> wrote:
> On Mon, May 18, 2020, sangita kachhap wrote:
> >
> >I am working on glycated oxy-hemoglobin.
> >I have generated parameters for oxy-heme and N-terminal glycated-Valine.
> >But when I am generating .prmtop and .inpcrd file, leap adding a "TER"
> card
> >between N-terminal glycated-Valine (first residue) and Histidine (second
> >residue).
> >
> >Since TER is adding within the chain, will it be problematic for further
> MD
> >simulation?
>
> You can use parmed to check if the bonding between the first and second
> residue is correct.
>
> Also, it's often safer to use ambpdb to create a pdb file from the
> prmtop and inpcrd files, rather than using tleap's savePdb command. See
> if that makes a difference for you.
>
> ....dac
>
>
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Received on Tue May 19 2020 - 13:00:02 PDT
