[AMBER] multiple residues and solvatebox command

From: Azade Yazdan Yar <azade.yazdanyar.gmail.com>
Date: Fri, 2 Dec 2016 13:24:22 +0100

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)


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,

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Received on Fri Dec 02 2016 - 04:30:02 PST
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