Dear Amber Users
I am trying to strip WAT from from multiple trajectory in single input and
then write strip topology file for that. For this I am using command like
this
#load topology
parm 0system/md_out/0SPC.top
parm 10system/md_out/10SPC.top parmindex 1
parm 20system/md_out/20SPC.top parmindex 2
parm 30system/md_out/30SPC.top parmindex 3
parm 40system/md_out/40SPC.top parmindex 4
parm 50system/md_out/50SPC.top parmindex 5
#load trajectory
trajin 0system/md_out/md_file/6_md5_0SPC.crd
trajin 10system/md_out/md_file/6_md5_10SPC.crd parmindex 1
trajin 20system/md_out/md_file/6_md5_20SPC.crd parmindex 2
trajin 30system/md_out/md_file/6_md5_30SPC.crd parmindex 3
trajin 40system/md_out/md_file/6_md5_40SPC.crd parmindex 4
trajin 50system/md_out/md_file/6_md5_50SPC.crd parmindex 5
#Action command
strip :SPC
strip :SPC parmindex 1
strip :SPC parmindex 2
strip :SPC parmindex 3
strip :SPC parmindex 4
strip :SPC parmindex 5
trajout ura_0SPC.crd
trajout ura_10SPC.crd parmindex 1
trajout ura_20SPC.crd parmindex 2
trajout ura_30SPC.crd parmindex 3
trajout ura_40SPC.crd parmindex 4
trajout ura_50SPC.crd parmindex 5
parmstrip :SPC
parmstrip :SPC parmindex 1
parmstrip :SPC parmindex 2
parmstrip :SPC parmindex 3
parmstrip :SPC parmindex 4
parmstrip :SPC parmindex 5
parmwrite out ura_0SPC.strip.parm7
parmwrite out ura_10SPC.strip.parm7 parmindex 1
parmwrite out ura_20SPC.strip.parm7 parmindex 2
parmwrite out ura_30SPC.strip.parm7 parmindex 3
parmwrite out ura_40SPC.strip.parm7 parmindex 4
parmwrite out ura_50SPC.strip.parm7 parmindex 5
but it is showing error
CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 06/24/15 17:40:01
| Available memory: 153.504 MB
INPUT: Reading Input from file ptraj4imin5
[parm 0system/md_out/0SPC.top ]
Reading '0system/md_out/0SPC.top' as Amber Topology
[parm 10system/md_out/10SPC.top parmindex 1]
Reading '10system/md_out/10SPC.top' as Amber Topology
[parm 20system/md_out/20tmoSPC.top parmindex 2]
Reading '20system/md_out/20tmoSPC.top' as Amber Topology
[parm 30system/md_out/30tmoSPC.top parmindex 3]
Reading '//30system/md_out/30tmoSPC.top' as Amber Topology
[parm/40system/md_out/40tmoSPC.top parmindex 4]
Reading '/40system/md_out/40tmoSPC.top' as Amber Topology
[parm /50system/md_out/50tmoSPC.top parmindex 5]
Reading '/50system/md_out/50tmoSPC.top' as Amber Topology
[trajin 0system/md_out/md_file/6_md5_0SPC.crd ]
Reading '0system/md_out/md_file/6_md5_0SPC.crd' as Amber Trajectory
[trajin 10system/md_out/md_file/6_md5_10SPC.crd parmindex 1]
Reading '10system/md_out/md_file/6_md5_10SPC.crd' as Amber Trajectory
[trajin 20system/md_out/md_file/6_md5_20SPC.crd parmindex 2]
Reading '20system/md_out/md_file/6_md5_20SPC.crd' as Amber Trajectory
[trajin 30system/md_out/md_file/6_md5_30SPC.crd parmindex 3]
Reading '30system/md_out/md_file/6_md5_30SPC.crd' as Amber Trajectory
[trajin 40system/md_out/md_file/6_md5_40SPC.crd parmindex 4]
Reading '40system/md_out/md_file/6_md5_40SPC.crd' as Amber Trajectory
[trajin 50system/md_out/md_file/6_md5_50SPC.crd parmindex 5]
Reading '50system/md_out/md_file/6_md5_50SPC.crd' as Amber Trajectory
[strip :SPC ]
STRIP: Stripping atoms in mask [:SPC]
[strip :SPC parmindex 1]
STRIP: Stripping atoms in mask [:SPC]
Error: [strip] Not all arguments handled: [ parmindex 1 ]
1 errors encountered reading input.
TIME: Total execution time: 0.0355 seconds.
As given on Amber 15 Reference Manual for trajin (29.7.1. ) command on page
541.
it will accept both parmindex or tag name during trajectory reading.
So I tried both in similar way, but in both case I am getting error.
Thank you in advance for your help
Regards
Rahman
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Received on Wed Jun 24 2015 - 06:00:05 PDT
