Sorry, you need to use the stripped topology of course:
> parm 1blb_dimer.prmtop
should instead be
parm strip.1blb_dimer.prmtop
which should have been generated in the previous step.
-Dan
> trajin strip.md.nc
> rms :1-185 first
> average chain1.pdb :1-185 pdb
> rms :186-366 first
> average chain2.pdb :186-366 pdb
>
> -Dan
>
> On Wed, Jan 7, 2015 at 12:39 PM, Ibrahim Said <saidibrahim569.gmail.com> wrote:
>> Dear Dan
>> My full script is
>> parm 1blb_dimer.prmtop
>> trajin 1blb_dimer-prod-1.mdcrd 1 50 1
>> -
>> -
>> -
>> strip :WAT
>> strip :Na+
>> average chain1.pdb :1-185 pdb
>> average chain2.pdb :186-366 pdb
>> trajout strip.md.nc netcdf
>> Also I did not see the previous massage.
>>
>> said
>>
>> On Wed, Jan 7, 2015 at 9:33 PM, David A Case <case.biomaps.rutgers.edu>
>> wrote:
>>
>>> On Wed, Jan 07, 2015, Ibrahim Said wrote:
>>>
>>> > I added the line parm protein.prmtop, but I did not get
>>> > strip.protein.prmtop.
>>>
>>> This sounds like progress, assuming that all the other error messages
>>> (relating to not being able to open the protein.prmtop file) are gone.
>>>
>>> > > > trajin 1blb_dimer-prod-1.mdcrd 1 50 1
>>> > > > -
>>> > > > -
>>> > > > -
>>> > > > trajin 1blb_dimer-prod-12.mdcrd 1 100 1
>>> > > > trajout strip.md.nc netcdf
>>>
>>> The above script doesn't have any "strip" commands in it. Are you actually
>>> expecting to strip atoms?
>>>
>>> If you want to get a stripped prmtop file (in addition to a stripped
>>> trajectory file), you need to have a "strip" line with the "outprefix"
>>> option.
>>> (And if you just want to combine several trajectory files into a single
>>> one,
>>> without stripping atoms, then there is no need to create a new prmtop
>>> file.)
>>>
>>> ...hope this helps...dac
>>>
>>>
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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)
--
-------------------------
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 Wed Jan 07 2015 - 12:30:03 PST
