Hi,
First, you can combine those two strip commands into a single strip
command. If you do indeed want a stripped topology file you need to
add the 'outprefix' keyword like Dave mentioned before, e.g.:
strip :WAT,Na+ outprefix strip
Also, be aware that your average structures as the script is now will
contain rotational and translational motion. You may want to create
the average structures in a separate run from your stripped trajectory
instead, with some rms-fitting to remove such motion from your
averages, e.g.:
parm 1blb_dimer.prmtop
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)
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Received on Wed Jan 07 2015 - 12:00:03 PST
