Hello Pierre,
I am not sure exactly what is going on with your execution. There were no
other errors reported during the leap execution? I am assuming that you
don't have any force-field related issues. Correct? I have done this
several times and haven't had a problem. If you wish, you can send me your
files privately and I can try to trouble shoot it.
Bests,
Karl
On Fri, Apr 10, 2015 at 3:51 AM, Pierre Bertin <bertinp71.gmail.com> wrote:
> Dear users,
>
> I am trying to solvate a carbon nanotube (CNT) in nitric acid (NIA) with
> AmberTools14.
> I red Mailing list Archives and I found solutions, however some errors are
> remaining.
>
> *Workflow* :
>
> *1)* Make a *PDB file* of CNT and NIA. *Complete*.
>
>
> *2) Convert* CNT and NIA molecules for AmberTools with : Antechamber. (I
> used acdoctor to check input molecule, and I have just 1 warning because
> atom name = atome type and can be ignored)
>
> I use the Amber format in tutorials : mol2.
> antechamber -i NIA.pdb -fi pdb -o NIA.mol2 -fo mol2 -c bcc -s 2
> antechamber -i CNT.pdb -fi pdb -o CNT.mol2 -fo mol2 -c bcc -s 2
>
>
> *3)* Tleap command to import molecules :
>
> *-- Initializing tleap : *
> tleap -f oldff/leaprc.ff99SB
> >source leaprc.gaff #All atoms
>
> *-- import molecules :*
> >NIA = loadmol2 NIA.mol2
> >check NIA
> >CNT = loadmol2 CNT.mol2
> >check CNT
>
>
> *-- Load params from frcmod files* (I do not know why NIA.frcmod is empty,
> just titles) :
> >loadamberparams NIA.frcmod
> >saveoff NIA nia.lib
> >saveamberparm NIA nia2.prmtop nia2.inpcrd
>
> >loadamberparams NIA.frcmod
> >saveoff CNT cnt.lib
> >saveamberparm CNT cnt.prmtop cnt.inpcrd
>
>
> And now, I try to solvate the CNT in NIA solvent.
>
> First, construction of the box for NIA:
> >setBox NIA vdw
> And then, solvate the CNT:
> >solvateBox CNT NIA 20
>
> I saw this in the mailing list archives. But I have a *fatal error *:
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> !FATAL
> ERROR----------------------------------------
> !FATAL: In file [varArray.c], line 156
> !FATAL: Message: VarArrayDestroy: VARARRAY is NULL!
> !ABORTING.
>
> """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
>
> If someone have already tried to solvate a molecule in organic solvent from
> imported molecule, I will be pleased to read his lines! ;)
>
> sincerely,
> Pierre.
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Apr 10 2015 - 00:30:03 PDT
