Hi,
Am I correct in assuming you are running in interactive mode? If that
is the case cpptraj will not run unless you tell it to (by typing
'run' or 'go'). So you can either repeat your input and type 'run' or
better yet put that input into a file and run with:
cpptraj -i inputfile
The advantage of the latter approach is that if you want to repeat the
calculation you don't have to enter all the commands again.
-Dan
On Wed, Jun 19, 2013 at 12:28 PM, Hailin Huang <hailin.huang.my.liu.edu> wrote:
> Hi Dan,
>
> I am not quite familiar with using cpptraj. Here is what I did:
>
>>parm 3TNP-with2ADPmg.prmtop
> Warning: Could not determine atomic number from mass (3.000000) [DX1 ]
> Warning: Could not determine atomic number from name [DX1 ]
> (more of these warnings are skipped)
>>trajin prod20.rst
> [prod20.rst] contains 1 frames.
>>autoimage
> AUTOIMAGE: To box center based on center of mass, anchor is first
> molecule.
>>trajout test20.rst
>>quit
>
> I could not get any output files. Could you correct me if I did anything
> wrong?
>
> Thank you,
> Richard
>
>
> On Wed, Jun 12, 2013 at 5:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> I suspect that the protein doesn't actually break apart - this is a
>> visual artifact caused by 'wrapping' the coordinates. You can use the
>> 'autoimage' command in cpptraj to re-image your solute back into the
>> primary cell.
>>
>> -Dan
>>
>> On Wed, Jun 12, 2013 at 2:56 PM, Hailin Huang <hailin.huang.my.liu.edu>
>> wrote:
>> > Dear Amber users,
>> >
>> > I am running a prodution simulation of protein 3TNP in a 10A solvatebox.
>> > After about 25 ns of simlutation time, part of the protein drifts out of
>> > the solvent box. As the protein falls out further it breaks apart
>> > eventually and the fragment comes back in from the other side of the
>> > solvent box. Will I solve this problem by simply increasing the size of
>> the
>> > solvent box? Is there a way to lock the protein within the box? Thanks
>> for
>> > any help!
>> >
>> > The input file follows
>> >
>> > &cntrl
>> > imin=0, irest=0, ntx=1,
>> > ntpr=2000, ntwx=2000, nstlim=2500000,
>> > dt=0.001, ntt=3, tempi=300,
>> > temp0=300, gamma_ln=1.0, ig=-1,
>> > ntp=0, ntc=2, ntf=2, cut=8,
>> > ntb=1, iwrap=1, ioutfm=1,
>> > /
>> >
>> > Regards,
>> > Richard
>> > _______________________________________________
>> > 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
--
-------------------------
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)
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Received on Wed Jun 19 2013 - 13:00:02 PDT
