Hello everyone
I am new to amber. So forgive me if my question is very simple.
I would like to put to unattached residues in a box of water.
For this purpose, first I used antechamber and parmchk2 to build the mol2
and frcmod files for the two residues.
Then I used xleap.
========================================
source leaprc.gaff
source leaprc.water.spce
loadamberparams frcmod.spce
residue_a = loadmol2 residue_a.mol2
residue_b = loadmol2 residue_b.mol2
loadamberparams residue_a.frcmod
loadamberparams residue_b.frcmod
edit residue_a
# here I import residue_2; so now: residue_a = residue_a + residue_b
solvatebox residue_a SPCBOX 12.0
saveamberparm residue_a prmtop inpcrd
=========================================
which leads to the following types of errors:
(type - hence mass - of one or more atoms could not be found)
and
For atom: .R<WAT 3406>.A<H2 3> Could not find vdW (or other) parameters for
type: HW
I understand that I might have forgot to load a library. But I cannot
figure out which one exactly.
It would be nice if you can tell me what I am doing wrong here?
And also, is the whole procedure reasonable or should I use another method
to put the two residues together?
Thanks a lot.
Best regards,
Azade
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Received on Fri Dec 02 2016 - 04:30:02 PST
