AMBER Archive (2008)

Subject: AMBER: problem with AMOEBA

From: j00323240_at_students.jsums.edu
Date: Wed Nov 26 2008 - 13:07:13 CST

Hello, all.

I am trying to solvate Adenine molecule with AMOEBA waters in AMBER 10.
First of all, ADE.prepin and ADE.frcmod files were generated by using RESP
charges with Antechamber tools. I used GAUSSIAN out-file instead of pdb.
Then, as usual, I loaded leaprc.amoeba and leaprc.gaff force fields
($AMBERHOME/exe/sleap command was used for such purpose), ADE.prepin and
ADE.frcmod files.
When it was a time to solvate my system, I typed
solvatebox ADE WATBOX 15

and following message shown up:
“Warning: unknown amber atom type 202, using radii 1.5
Warning: unknown amber atom type 203, using radii 1.5
Warning: unknown amber atom type 203, using radii 1.5…..
…..and so on”

After next command
Saveamoebaparm ADE ADE.prmtop ADE.inpcrd
I got
“get typeid of -1
sleap: component.cpp:421: bool mort::component_t::get_iptr(const
mort::hashid_t&, int, const int*&) const: Assertion `absid >=0 && absid <
m_idcounter' failed.
Aborted”
Does anyone have an idea what was wrong?

Thank you in advance, Al'ona Furmanchuk.

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