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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Received on Thu Apr 09 2015 - 19:00:02 PDT
