Hi,
Exactly, I want to run pmemd using final trayectory (.mdcrd) instead
firsts coordinates (.crd). For example, this is my script:
#!/bin/bash
################################
#SBATCH -t 10:00:00
#SBATCH -n 24
#SBATCH -p cola-corta,thinnodes
# SBATCH -p gpu-shared --gres=gpu
#initialdir = /home/csic/car/mtr/myriam/smp-195ptn4syn
########################
module load intel/2016.4.258 impi/5.1.3.223
amber/16-at-17-patchlevel-10-15-cuda
####
srun pmemd.MPI -O -i ./min-tar/min_wat.in -p
./leap/smp-195-ptn4rig.top -c ./leap/smp-195-ptn4rig.crd -r
./min-tar/smp-195-ptn4rig_min_wat_tar.rst -o
./min-tar/smp-195-ptn4rig_min_wat_tar.out -inf
./min-tar/smp-195-ptn4rig_min_wat_tar.info -e
./min-tar/smp-195-ptn4rig_min_wat_tar.enr -ref
./leap/smp-195-ptn4rig.crd
And I want run this:
#!/bin/bash
################################
#SBATCH -t 10:00:00
#SBATCH -n 24
#SBATCH -p cola-corta,thinnodes
# SBATCH -p gpu-shared --gres=gpu
#initialdir = /home/csic/car/mtr/myriam/smp-195ptn4syn
########################
module load intel/2016.4.258 impi/5.1.3.223
amber/16-at-17-patchlevel-10-15-cuda
####
srun pmemd.MPI -O -i ./min-tar/min_wat.in -p
./leap/smp-195-ptn4rig.top -c ./vcte/smp-195-ptn4rig_vcon3.mdcrd -r
./min-tar/smp-195-ptn4rig_min_wat_tar.rst -o
./min-tar/smp-195-ptn4rig_min_wat_tar.out -inf
./min-tar/smp-195-ptn4rig_min_wat_tar.info -e
./min-tar/smp-195-ptn4rig_min_wat_tar.enr -ref
./vcte/smp-195-ptn4rig_vcon3.mdcrd
Is it correct?
Thanx in advance
Myriam
Daniel Roe <daniel.r.roe.gmail.com> escribió:
> Hi,
>
> You haven't told us exactly what you have done, so I'm just guessing
> here, but it seems like you're trying to run sander or pmemd using a
> *trajectory* file in place of starting coordinates (i.e. you're
> specifying a trajectory file for '-c'). You need to provide a proper
> ASCII or NetCDF restart file for '-c'.
>
> -Dan
>
>
> On Tue, Dec 10, 2019 at 7:27 AM MYRIAN TORRES RICO
> <myriam.torres.iiq.csic.es> wrote:
>>
>>
>> Hi,
>>
>> I have a problem with my MD-tar. I have launched the scritps and I
>> have obtained this error:
>>
>>
>> ERROR: NetCDF restart has Conventions that are not AMBERRESTART.
>> ERROR: Could not read second line of ./vcte/smp-195-ptn4rig_vcon3.mdcrd
>>
>>
>> I have reviewed the file and apparently everything is fine...any idea?
>>
>> Thanx in advance!
>>
>>
>> Myriam
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Dec 11 2019 - 08:30:01 PST
