[AMBER-Developers] Problems in sleap

From: Ben Roberts <ben.roberts.geek.nz>
Date: Wed, 30 Mar 2011 16:42:51 -0400

Hi all,

Robert Smith has reported, on the main Amber list, some problems that he ran into when using sleap. I've been able to reproduce those problems (albeit that they're presented slightly differently) on the development tree.

1. Problems loading leaprc.amoeba
   ------------------------------

If I run this:

[gtkleap]$ source leaprc.amoeba

I get this result:

loadoff amoeba_amino.off
loadoff amoeba_aminont.off
loadoff amoeba_aminoct.off
loadoff amoeba_watbox.off
loadamoebaparams amoebapro09v4.prm
Assertion failed: (atomid==atomff.natom()+1), function mort::ambfrc::amoeba::read_atom, file ambfrc-amoeba.cpp, line 35.
Abort trap

On the other hand, if I do this:

[gtkleap]$ source $AMBERHOME/AmberTools/test/sleap/amoeba/leaprc.amoeba

I get this result:

loadoff amoeba_amino.off
loadoff amoeba_aminont.off
loadoff amoeba_aminoct.off
loadoff amoeba_watbox.off
loadamoebaparams amoebapro.prm
<snip>
[gtkleap]$

So that just works (maybe).

The difference appears to be in the file amoebapro09v4.prm, which, if I load manually, also gets me into hot water (specifically, the ASSERT described above).


2. Problems checking a molecule with the Amoeba force field
   --------------------------------------------------------

If I try to load a molecule and then run "check" on it, I get this message:

[gtkleap]$ check mol
check mol
all checks requested
Checking unit "mol"
Error: molecule _amberffp could not be found in the database!

This is after I've sourced a "leaprc.amoeba" file. Is a data structure other than _amberffp used if the amoeba force field is requested? If so, perhaps "check" needs to be revised accordingly.

3. Problems writing output (prmtop and inpcrd)
   -------------------------------------------

If I forget the check, and just go directly for loading parameters etc., I get this:

[gtkleap]$ source $AMBERHOME/AmberTools/test/sleap/amoeba/leaprc.amoeba
<snip>
[gtkleap]$ mol = loadmol2 em_ac.mol2
mol = loadmol2 em_ac.mol2
[gtkleap]$ mods = loadAmoebaParams em_ac.frcmod
mods = loadAmoebaParams em_ac.frcmod
[gtkleap]$ saveAmoebaParm mol prmtop inpcrd
saveAmoebaParm mol prmtop inpcrd
get typeid of -1
Error (get_iptr): while retrieving parameter typeid, impossible abs ID (-1)

In his original report, Robert got the even less comprehensible result:

get typeid of -1
sleap: data.cpp:424: bool mort::mcmpdata_t::get_iptr(const mort::hashid_t&,
int, const int*&) const: Assertion `absid >=0 && absid < m_idcounter'
failed.
Aborted

Could a fix for these problems be arrived at?

Thanks,
Ben

PS. I've attached Robert's files as slightly adjusted by me.



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Received on Wed Mar 30 2011 - 14:00:03 PDT
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