Hello,
I have attached the dihe.restraint file. I believe what is supposed to happen is the sed line should replace the FC from the dihe.restraint file with the string of numbers and that would be the restraints that pmemd should be reading. For some reason however, it seems as though it isn't being able to comprehend that. If you could take a look to see whether that is something that is within the scope of pmemd or if my syntax is the problem, that would be greatly appreciated!
For your reference:
Part in the submit file that tells pmemd where to see the restraints: sed -e "s/FC/{'250.0', '100.0' , '50.0' , '50.0' , '25.0'}/g \ sed 's/"[[:space:]]\+"/","/g" dihe.restraint > step6.1_equilibration.rest
FC = corresponds to an empty space in the dihe.restraint file.
Thank you,
Aanshi Gandhi (she/her)
M.ASc Candidate, Garton Lab
Email <mailto:aanshi.gandhi.mail.utoronto.ca> | LinkedIn <
https://www.linkedin.com/in/aanshigandhi/>
On 2021-03-29, 12:58 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:
EXTERNAL EMAIL:
this is complicated because it looks to me like the problem is not
related to Amber.
Looking at your md output file, it seems that your positional restraints
are read ok (but only you can tell if these are the right atoms). The
problem seems to be in reading the dihedral restraint file (is this what
you are calling the "rest" file?). See this important section from the
mdout:
*Restraints will be read from file: step6.2_equilibration.restHere are
comments from the DISANG input file: ** No
restraint defined ***
So pmemd is telling you that it did not read any restraints from that file.
It may be a formatting issue, or a problem in the script that sets up that
file. The script doesn't look like it came from an Amber program, so you'll
need to debug that and see what might be wrong. You didn't include that
file so we can't really check and see if it looks like something that pmemd
should be able to read.
On Mon, Mar 29, 2021 at 11:47 AM Aanshi Gandhi <
aanshi.gandhi.mail.utoronto.ca> wrote:
> Hello!
>
> I’m trying to run an MD simulation using AMBER outputs from CHARMM-GUI and
> I seem to be having some problems with my restraint files (.rest). I’ve
> attached the files for your consideration. A breakdown of what is happening:
>
> The minimization step worked fine. The first equilibration step; there’s a
> command in the README file to do: if (-e dihe.restraint && ${cnt} <
> ${cntmax}) sed -e "s/FC/${fc[${cnt}]}/g" dihe.restraint > ${istep}.rest.
> However, I got an error when I ran this on Beluga but when I removed the if
> command and just submitted it as: sed -e "s/FC/{'250.0', '100.0' , '50.0' ,
> '50.0' , '25.0'}/g \ sed 's/"[[:space:]]\+"/","/g" dihe.restraint >
> step6.1_equilibration.rest, it ran properly but it gave me an empty .rest
> file but a new file with the right information. Then, in the second
> equilibration step, I ran the same command as above and it ran completely
> fine except the .rest file was empty and there was no other file with the
> right information. However, the third equilibration step still ran without
> problems except again no .rest file.
>
> I would really appreciate any insight you may have on what I can do to fix
> this issue. I have attached my submit script for the second equilibration
> step (submit3.sh), the equilibration input file
> (step6.2_equilibriation.mdin), the empty rest file
> (step6.2_equilibration.rest), the output file
> (step6.2_equilibriation.mdout) and the README file from CHARMM.
>
> Thank you,
> Aanshi Gandhi (she/her)
> M.ASc Candidate, Garton Lab
> Email<mailto:aanshi.gandhi.mail.utoronto.ca> | LinkedIn<
> https://www.linkedin.com/in/aanshigandhi/>
>
>
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>
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Received on Mon Mar 29 2021 - 11:00:02 PDT
