My initial reaction is that there's no "TER" card in the receptor.pdb
file. Adding such a card after the protein component seems to solve the
problem when I run your file through tleap. Kind of surprising that tleap,
in all its detail and ability to fill out missing atoms, doesn't catch
stuff like this.
Dave
On Wed, Dec 5, 2018 at 6:27 PM Thomas Evangelidis <tevang3.gmail.com> wrote:
> Greetings,
>
> I am curious why when I load a pdb of crystal structure without hydrogens,
> tleap does not add OXT at the C-terminus. I have to save the structure to a
> new pdb file, load it and then tleap adds the OXT. Is there any way to skip
> the intermediate writing/loading step?
>
> Below is an example tleap script. I have also attached the receptor.pdb
> file but I don't know if it can go through the mailing list.
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> loadamberparams frcmod.ions1lm_126_tip3p
> loadamberparams frcmod.ions234lm_126_tip3p
> protein1 = loadpdb receptor.pdb
> savePDB protein1 protein1.pdb
> protein2 = loadpdb protein1.pdb
> savePDB protein2 protein2.pdb
> quit
>
> Thanks in advance.
> Thomas
>
>
> --
>
> ======================================================================
>
> Dr Thomas Evangelidis
>
> Research Scientist
>
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
> of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
> Prague, Czech Republic
> &
> CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
> Brno, Czech Republic
>
> email: tevang3.gmail.com
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> _______________________________________________
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>
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Received on Wed Dec 05 2018 - 17:00:02 PST
