Turns out that I was not the only one struggling with this one, it seems that the code syntax and indentation does not apply to EOF.
So, the closing EOF should NOT be indented
#!/bin/sh
> x=1
> while [ $x -le 100 ]
> do
> y=10
> while [ $y -le 100 ]
> do
> cpptraj << EOF
> parm *.prmtop
> trajin nvt'$y'ns.rst
> reference nvt'$y'ns.rst
> strip "!((:'$x' <: 8) & ! :'$x')"
> outtraj host_brt_'$x'_'$y'ns.pdb
> unstrip
> strip "!(:'$x')"
> outtraj guest_brt_'$x'_'$y'ns.pdb
> run
EOF
> y=$(( y + 10 ))
> done
> x=$(( x + 1 ))
> done
And then it runs, no more copy/paste
// Gustaf
> On 14 Aug 2019, at 14:28, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Well, I missed it completely. I was so hung upon the “mask” part that I did not carefully read the “important” section regarding distance based masks.
>
> It should now churn along using some loops:
>
> x=1
> while [ $x -le 100 ]
> do
> y=10
> while [ $y -le 100 ]
> do
> cpptraj << EOF
> parm *.prmtop
> trajin nvt'$y'ns.rst
> reference nvt'$y'ns.rst
> strip "!((:'$x' <: 8) & ! :'$x')"
> outtraj host_brt_'$x'_'$y'ns.pdb
> unstrip
> strip "!(:'$x')"
> outtraj guest_brt_'$x'_'$y'ns.pdb
> run
> EOF
> y=$(( y + 10 ))
> done
> x=$(( x + 1 ))
> done
>
> Sadly I am not enough of a programer to get the EOF part to work inside a bash script (unexpected EOF) and I have not figured out how to “pipe” commands into cpptraj so there is some copy/paste manoeuvring going on. Still, it beats making 1000 files myself :-)
>
> All the best and thank you again Dan!
> // Gustaf
>
>> On 14 Aug 2019, at 13:30, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Sorry - I had forgotten that selection by distance requires a reference
>> structure (for further details see the reference manual). Just add a
>> ‘reference nvt10.ns.rst7’ after the ‘parm’.
>>
>> Hope that helps,
>>
>> -Dan
>>
>> On Wed, Aug 14, 2019 at 5:32 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>>> Well, it seemed fully logical and this is likely shell related. Sadly, I
>>> seem unable to figure out how to get the suggested command sequence to
>>> execute correctly
>>>
>>> The
>>>
>>> strip "!((:1 <: 5) & ! :1)"
>>>
>>> command produces an error:
>>>
>>> No reference set, cannot select by distance
>>>
>>> Meaning that I get the "guest" file correctly and I do get the “host”
>>> file, however the only thing striped is :1 and every other molecule is
>>> there. I have tried varying or skipping “ and ‘ though this produces other
>>> errors where all of the mask is not read or I have “unmatched” parenthesise
>>> though I cannot see this in the commands.
>>>
>>> I have pretty much tried every combination of apostrophes and escape
>>> characters I can remember without any luck so once again I am looking for
>>> some input from people smarter then me.
>>>
>>> Best regards
>>> // Gustaf
>>>
>>>
>>>
>>>> On 12 Aug 2019, at 20:05, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> You could use the 'mask' command or you could use a combination of
>>>> 'strip'/'unstrip' and 'outtraj' (which is what I usually do). E.g.
>>>>
>>>> cpptraj <<EOF
>>>> parm *.prmtop
>>>> trajin nvt10.ns.rst7
>>>> strip "!((:1 <: 5) & ! :1)"
>>>> outtraj host.pdb
>>>> unstrip
>>>> strip "!(:1)"
>>>> outtraj guest.pdb
>>>> run
>>>> EOF
>>>>
>>>> Note that I'm negating your original masks, which effectively turns
>>>> 'strip' into "keep".
>>>>
>>>> Hope this helps,
>>>>
>>>> -Dan
>>>>
>>>> On Wed, Aug 7, 2019 at 9:43 AM Gustaf Olsson <gustaf.olsson.lnu.se>
>>> wrote:
>>>>>
>>>>> Hang on one second
>>>>>
>>>>> Since there was a flag allowing reading the .nrst file, maybe I don’t
>>> need to convert and pass to ambmask for my purpose as the “mask” available
>>> in cpptraj should work just fine.
>>>>>
>>>>> What I am doing right now is the following:
>>>>>
>>>>> $ ambmask -p *.prmtop -c nvt10ns.rst7 -prnlev 0 -out pdb -find
>>> '(:1 <: 5) & ! :1' > host.pdb
>>>>> $ ambmask -p *.prmtop -c nvt10ns.rst7 -prnlev 0 -out pdb -find
>>> ':1' > guest.pdb
>>>>>
>>>>> This works fine, printing every residue within 5 angstroms from 1
>>> excluding 1 itself to one “host” file and just residue 1 to another “guest”
>>> file which can then be used to set up docking runs.
>>>>>
>>>>> Can I not just use the mask function in cpptraj (which seems identical)
>>> to accomplish the same thing? Reading in the .nrst files as described and
>>> then creating the same output and then skipping the in-between step of file
>>> conversion?
>>>>>
>>>>> Best regards
>>>>> // Gustaf
>>>>>
>>>>>
>>>>>> On 7 Aug 2019, at 14:06, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>>>>
>>>>>> cpptraj -p topology.parm7 -y restart.nrst -x restart.rst7
>>>>>>
>>>>>> -Dan
>>>>>>
>>>>>> On Wed, Aug 7, 2019 at 7:41 AM Gustaf Olsson <gustaf.olsson.lnu.se>
>>> wrote:
>>>>>>>
>>>>>>> As the title states, a lazy search for a shortcut so as not having to
>>> figure it out by myself.
>>>>>>>
>>>>>>> What would be the "most scriptable”, non-GUI and fast way to convert
>>> from NCRST to old RST(7) format using anything available in the
>>> amber/ambertools package?
>>>>>>>
>>>>>>> I need to convert a number of new binary format to the old ASCII
>>> format to process with another program.
>>>>>>>
>>>>>>> Best regards
>>>>>>> // Gustaf
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>> _______________________________________________
>>> 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
>
> _______________________________________________
> 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
Received on Wed Aug 14 2019 - 06:30:03 PDT
