>From the Amber 15 user manual, section 3.9 (Ions):
"Please note: Many leaprc files load the atomic_ions.lib file, but you
will still need to explicitly load a frcmod file that matches the
water model you are using."
So you are probably missing a 'loadamberparams <file>' command, where
<file> corresponds to the ion model you wish to use. See the Amber
manual for a complete listing.
Hope this helps,
-Dan
On Mon, Aug 17, 2015 at 8:14 AM, mohammad r <mohammad.r0325.yahoo.com> wrote:
> Hi;
> When I neutralize my solvate box ( with addionsrand command: "addIonsRand mol CL 0") then try to get the topology and coordinate files with saveamberparm command, I receive this error:> saveamberparm mol topol.top coor.crd
> Checking Unit.
> Building topology.
> Building atom parameters.
> For atom: .R<CL 8306>.A<CL 1> Could not find vdW (or other) parameters for type: Cl-
> For atom: .R<CL 8307>.A<CL 1> Could not find vdW (or other) parameters for type: Cl-
> For atom: .R<CL 8308>.A<CL 1> Could not find vdW (or other) parameters for type: Cl-
> For atom: .R<CL 8309>.A<CL 1> Could not find vdW (or other) parameters for type: Cl-
> For atom: .R<CL 8310>.A<CL 1> Could not find vdW (or other) parameters for type: Cl-
> For atom: .R<CL 8311>.A<CL 1> Could not find vdW (or other) parameters for type: Cl-
> For atom: .R<CL 8312>.A<CL 1> Could not find vdW (or other) parameters for type: Cl-
> Parameter file was not saved. I don't know what to do?
> Thank you much, Mohammad.
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Aug 17 2015 - 08:30:03 PDT
