From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jan 09 2015 - 02:31:55 CST
Silly mistake, .rsd instead of .rst
thanks
francesco
On Wed, Jan 7, 2015 at 10:28 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Are you sure the file is there and has permission to be read?
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Francesco Pietra
> *Gesendet:* Mittwoch, 7. Januar 2015 09:55
> *An:* NAMD
> *Betreff:* namd-l: Failure MD with par7/rst7 amber input
>
>
>
> Hi:
>
> with namd 2.10 error in trying GBIS minimization of par7/rst7 amber input
>
> Reading parm file (./PROT.parm7) ...
> PARM file in AMBER 7 format
> Warning: Skipping ATOMIC_NUMBER in parm file while seeking MASS.
> Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY.
> Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY.
> Warning: Encounter 10-12 H-bond term
> Warning: Found 919 H-H bonds.
> Command = zcat ./PROT.rst7.Z
> Filename.Z = ./PROT.rst7.Z
> Command = gzip -d -c ./PROT.rst7.gz
> Filename.gz = ./PROT.rst7.gz
> FATAL ERROR: Can't open AMBER coordinate file!: No such file or directory
>
> min-01.conf contains:
>
> # AMBER force field
> amber on # expect to read parm7 file
> parmfile ./PROT.parm7 #input parm7 file from xleap
> ambercoor ./PROT.rst7 # input coordinate file from xleap
>
> Notice that I got minimization of the active center of PROT by using the
> same GBIS minimization file layout.
>
> Is "rst7" now confusing the parser?
>
> thanks for advice
>
> francesco pietra
>
>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:20:47 CST