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
>>>>
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Received on Wed Aug 14 2019 - 03:00:03 PDT
