You have ioutfm=1 in your mdin, so it should write netcdf format restart
which won't be text readable but should still be fine for continuing the
run. Maybe try reading it in cpptraj and see if it is recognized as netcdf.
It can be converted to text format with cpptraj if needed.
On Tue, Jun 22, 2021, 3:37 PM GALLO FACUNDO NAHUEL <
fgallo.cibion.conicet.gov.ar> wrote:
> Hi! I'm having trouble when running a ligand-protein MD simulation. For
> one specific ligand, when I run the first equilibration (eqv) the .rst7
> coordinate file is nonsense. The same .mdin equilibration file works for
> all the other ligands in the same system, and the coordinates in the .rst7
> files are correctly written, so it seems to be something wrong with the
> ligand.
> The .mdin used is:
>
>
> &cntrl
> IMIN=0,NMROPT=0,
> NTX=1,IREST=0,
>
> NTWR=100000,NTPR=20000,NTWX=20000,NTWV=0,NTWE=0,IWRAP=0,IOUTFM=1,NTXO=1,
> NTR=1,RESTRAINT_WT=50.0,RESTRAINTMASK=':1-633',
> MAXCYC=0,NTMIN=1,
> NSTLIM=100000,DT=0.0001,NRESPA=1,
> NTT=3,TEMPI=0.0,TEMP0=10.0,VLIMIT=-1.0,GAMMA_LN=5.0,IG=-1,
> NTP=0,PRES0=1.0,TAUP=1.0,
> NTC=1,
> NTF=1,NTB=1,CUT=8.0,IFQNT=0,IGB=0,
> /
>
> And the .rst7 written is something like:
>
> default_name
>
> 143939 0.1000000E+02
> ************************************************************************
> ************************************************************************
> ************************************************************************
> ************************************************************************
> ************************************************************************
> ************************************7943.2606719************************
> ************************************************************************
> ************************************8664.4607917************************
>
> The .out file doesn't show any error so it seems the equilibration is
> being performed but the .rst7 output file is not.
> Thanks in advance
>
> Facu
>
> _______________________________________________
> 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 Tue Jun 22 2021 - 15:30:02 PDT
