[AMBER] Packmol and Amber

From: emanuele falbo <falbo.emanuele.gmail.com>
Date: Tue, 24 Sep 2019 14:33:12 +0100

Dear all,

I managed to create an file.xyz with multiple of my molecules by using
Afterwards, I do convert the file.xyz into a file.mol2 and generate the
topology and coordinates with tleap.

*source leaprc.water.tip3pparam = loadamberparams frcmod.h4li8 # ad-hoc
parameter for my molecule*

*guest = loadmol2 file.mol2 *

*listcheck guest#addIons2 guest LI 0solvateBox guest TIP3PBOX 12.0
saveamberparm guest out.prmtop out.rst7quit*

However, when running a dynamics sander gives me the following error:

*Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM*

So, I have reason to believe that the number of molecules under the
ATOMS_PER_MOLECULE" doesn't give the total nr. of atoms in the system,
however, I do not know what could make this happen, and eventually how to
fix it.

Do you have any useful suggestions of what I am doing wrong? Any help would
be much appreciated.


*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Tue Sep 24 2019 - 07:00:03 PDT
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