[AMBER] tleap does not add OXT when I load a crystal structure

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Thu, 6 Dec 2018 00:23:47 +0100


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

Thanks in advance.

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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Received on Wed Dec 05 2018 - 15:30:03 PST
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