Dear Amber users and developers,
I am trying to use AMOEBA force field the same way as I use FF03.
Here is commands which I tried to run:
====================================================
$AMBERHOME/exe/sleap
source leaprc.amoeba
2trx = loadpdb 2trx.pdb
saveamoebaparm 2trx bb.top bb.xyz
====================================================
After the last command I got:
====================================================
saveamoebaparm 2trx bb.top bb.xyz
get typeid of -1
sleap: component.cpp:432: bool mort::component_t::get_iptr(const long long
&, int, const int *&) const: Assertion `absid >=0 && absid < m_idcounter'
failed.
Aborted
====================================================
Also, the command "addions 2trx Na+ 0" doesn't work. The result is:
====================================================
addions 2trx Na+ 0
sleap: ../freelib/boost/shared_ptr.hpp:247:
boost::detail::shared_ptr_traits<T>::reference
boost::shared_ptr<T>::operator*() const [with T = mort::molecule_t]:
Assertion `px != 0' failed.
Aborted
====================================================
The same is with solvation:
====================================================
solvatebox 2trx WATBOX 10.0
Warning: no amber force field has been loaded, VDW radii set to 1.5.
...
====================================================
I tested the example from .../amber10/test/sleap/amoeba for jac_2.pdb and
didn't get any problem.
I can't figure out what I am doing wrong.
I use Amber 10, Amber Tools 1.2.
I attached my pdb file.
Any advice and help will be appreciated.
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Received on Thu Sep 23 2010 - 13:00:09 PDT
