Dear all,
I managed to create an file.xyz with multiple of my molecules by using
packmol.
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.
Cheers,
Manuele
--
*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/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 24 2019 - 07:00:03 PDT
