Dear Jason,
I want one suggestion, if I replace arsenic with phosphorus (they belong to
same group) and prepare frcmod and prepin files (it will be easy for amber
library), thereafter again replace phosphorus with arsenic and correct the
bond angles, length, dihedral etc from Gaussian optimized file, and then
proceed for further simulation, what will be validations of such procedure?
Will it be appropriate?
Thanks and regards
Kshatresh
On Sat, Mar 2, 2013 at 11:58 PM, Kshatresh Dutta Dubey
<kshatresh.gmail.com>wrote:
> No, they are of one or two letter.
>
>
> On Sat, Mar 2, 2013 at 11:52 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Do any of the atom types in your frcmod file have more than 2 letters in
>> them?
>>
>> On Sat, Mar 2, 2013 at 4:03 AM, Kshatresh Dutta Dubey
>> <kshatresh.gmail.com>wrote:
>>
>> > Hi Daniel
>> >
>> > Thanks for your reply. I am using Amber Tool 1.5, i.e amber 11. I used
>> > folowing commands for antechamber-
>> > antechamber -i input.gout -fi gout -o output.prepin -fo prepi -c resp
>> -s 2
>> > -j both -at amber -rn AS
>> > parmchk -i output.prepin -f prepi -o output.frcmod
>> >
>> > and following commands for Leap section
>> > tleap
>> > >source leaprc.ff10
>> > >source leaprc.gaff
>> > >loadamberprep output.prepin
>> > Loading Prep file: ./output.prpin
>> > >loadamberparams output.frcmod
>> > Loading parameters: ./output.frcmod
>> > Reading force field modification type file (frcmod)
>> > Reading title:
>> > remark goes here
>> > !FATAL ERROR----------------------------------------
>> > !FATAL: In file [varArray.c], line 182
>> > !FATAL: Message: Realloc: Cannot allocate memory!
>> > !ABORTING.
>> >
>> > Thanks in adavance
>> > kshatresh
>> >
>> >
>> > On Fri, Mar 1, 2013 at 8:14 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >
>> > > Hi,
>> > >
>> > > Could you list the exact commands you used and the output (including
>> > > any error messages) that it produced? Also, what version of AmberTools
>> > > are you using, and have all bugfixes been applied?
>> > >
>> > > -Dan
>> > >
>> > > On Fri, Mar 1, 2013 at 6:28 AM, Kshatresh Dutta Dubey
>> > > <kshatresh.gmail.com> wrote:
>> > > > Dear All,
>> > > >
>> > > > I have to simulate Arsenite, As(OH)3, using Amber. I optimized the
>> > > > structure using Gaussian and calculated ESP fitting. I successfully
>> > > > generated the prepin and frcmod files using antechamber and resp
>> > > procedure.
>> > > > Unfortunately, I am unable to generate corresponding topology and
>> > > > coordinate file using Leap. During the process, leap accepts prepin
>> > file
>> > > > but the it is unable to load corresponding frcmod file.
>> > > > Please help me to solve this issue.
>> > > > Thanks in advance
>> > > >
>> > > > Kshatresh
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > >
>> > >
>> > > --
>> > > -------------------------
>> > > Daniel R. Roe, PhD
>> > > Department of Medicinal Chemistry
>> > > University of Utah
>> > > 30 South 2000 East, Room 201
>> > > Salt Lake City, UT 84112-5820
>> > > http://home.chpc.utah.edu/~cheatham/
>> > > (801) 587-9652
>> > > (801) 585-9119 (Fax)
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sat Mar 02 2013 - 11:00:03 PST
