And you will also need to specify you coordinate file so that you command line will read:
$AMBERHOME/exe/sander -O -i Mggvvia_gb_init_min.in -o Mggvvia_gb_init_min.out -p Mggvvia_vac.prmtop -c Mggvvia_vac.inpcrd -r Mggvvia_gb_init_min.rst
Pete
>>> On 5/24/2009 at 2:28 PM, in message <86ad38fa0905241128o2b3b26b9l5c09d9d60577c078.mail.gmail.com>, Alessandro Nascimento <al.s.nascimento.gmail.com> wrote:
Try using "-p" *.prmtop instead of "-c". Or, as posted for your case:
$AMBERHOME/exe/sander -O -i Mggvvia_gb_init_min.in -o
Mggvvia_gb_init_min.out -p
Mggvvia_vac.prmtop -r Mggvvia_gb_init_min.rst
Hope that helps,
--alessandro
On Sun, May 24, 2009 at 2:27 PM, Workalemhu Berhanu
<wberhanu.mail.ucf.edu> wrote:
> Dear all
>
> Hi
> I am new to the amber software and I am using amber9. When Load my pdb file in xleap it went well and created the topology and Cartesian coordinate. But when in used the top and crd file to run minimization of the created structure in sander it is not working and it says Unit 8 Error on OPEN: prmtop. Could please help in figuring out what went wrong? Thank you
>> model = loadpdb "Mggvvia.pdb"
> Loading PDB file: ./Mggvvia.pdb
> total atoms in file: 36
> Leap added 42 missing atoms according to residue templates:
> 42 H / lone pairs
>> saveamberparm model Mggvvia_vac.prmtop Mggvvia_vac.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 11 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CALA 1
> NGLY 1
> )
> (no restraints)
> $AMBERHOME/exe/sander -O -i Mggvvia_gb_init_min.in -o Mggvvia_gb_init_min.out -c
Mggvvia_vac.prmtop -r Mggvvia_gb_init_min.rst
>
> Unit 8 Error on OPEN: prmtop
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
[ ]s
--alessandro
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Received on Mon May 25 2009 - 01:11:19 PDT
