AMBER Archive (2006)

Subject: Re: AMBER: RMSd error

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• In reply to: Claire Zerafa: "AMBER: RMSd error"
• Next in thread: Claire Zerafa: "Re: AMBER: RMSd error"
• Reply: Claire Zerafa: "Re: AMBER: RMSd error"
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it would help if you replied to the last mail I posted about
this. tell us how many FRAMES you have, not how many ps.
I can't really understand what's going wrong unless you are
very specific. are you saying that ptraj tells you it is writing
3598 values but the file does not have 3598 values?
did you try removing the old rmsd output and rerunning ptraj?
is there sufficient disk space available? are you using quotas?

Claire Zerafa wrote:

> Hi All,,
> >
> > I am still trying to figure out why I do not produce PMSd data for
> the entire trajectory that I am reading in ptraj. I am enclosing the
> output file from ptraj below. I still cannot identify any errors. It
> seems that all sets were read in, and
> > that the output file was generated correctly. Just I get RMSd
> valvues for 719ps out or a total of 1820ps I simulated. Can anyone
> pick up what I am missing please?
> >
> > Thanks
> >
> > Claire
> >
> > Amber8 Module: ptraj
> >
> > CYX GLN PRO ILE PHE LEU ASN VAL LEU GLU
> > ALA ILE GLU PRO GLY VAL VAL CYS ALA GLY
> > HIE ASP ASN ASN GLN PRO ASP SER PHE ALA
> > ALA LEU LEU SER SER LEU ASN GLU LEU GLY
> > GLU ARG GLN LEU VAL HIE VAL VAL LYS TRP
> > ALA LYS ALA LEU PRO GLY PHE ARG ASN LEU
> > HIE VAL ASP ASP GLN MET ALA VAL ILE GLN
> > TYR SER TRP MET GLY LEU MET VAL PHE ALA
> > MET GLY TRP ARG SER PHE THR ASN VAL ASN
> > SER ARG MET LEU TYR PHE ALA PRO ASP LEU
> > VAL PHE ASN GLU TYR ARG MET HIE LYS SER
> > ARG MET TYR SER GLN CYS VAL ARG MET ARG
> > HIE LEU SER GLN GLU PHE GLY TRP LEU GLN
> > ILE THR PRO GLN GLU PHE LEU CYS MET LYS
> > ALA LEU LEU LEU PHE SER ILE ILE PRO VAL
> > ASP GLY LEU LYS ASN GLN LYS PHE PHE ASP
> > GLU LEU ARG MET ASN TYR ILE LYS GLU LEU
> > ASP ARG ILE ILE ALA CYX LYS ARG LYS ASN
> > PRO THR SER CYS SER ARG ARG PHE TYR GLN
> > LEU THR LYS LEU LEU ASP SER VAL GLN PRO
> > ILE ALA ARG GLU LEU HIE GLN PHE THR PHE
> > ASP LEU LEU ILE LYS SER HIE MET VAL SER
> > VAL ASP PHE PRO GLU MET MET ALA GLU ILE
> > ILE SER VAL GLN VAL PRO LYS ILE LEU SER
> > GLY LYS VAL LYS PRO ILE TYR PHE HIE THR
> > BEN WAT WAT WAT WAT WAT WAT WAT WAT WAT
> > WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
> > ...
> > WAT
> > Scanning Box
> > Successfully completed readParm.
> >
> > PTRAJ: Processing input file...
> > Input is from standard input
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md2.mdcrd.gz
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md3.mdcrd.gz
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md4.mdcrd.gz
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md5.mdcrd.gz
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md6.mdrcd.gz
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md7.mdrcd.gz
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md8.mdcrd.gz
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md9.mdcrd.gz
> >
> > PTRAJ: trajin
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_10.mdrcd.gz
> >
> > PTRAJ: rms first out
> > /DATA/VINCLOZOLIN_TRAJECTORY_ANALYSIS/vinclozolin_backbone.rms @CA
> time 0.2
> > Mask [@CA] represents 250 atoms
> >
> > PTRAJ: strip :WAT
> > Mask [:WAT] represents 21090 atoms
> > FYI: No output trajectory specified (trajout), none will be saved.
> >
> > PTRAJ: Successfully read the input file.
> > Coordinate processing will occur on 3598 frames.
> > Summary of I/O and actions follows:
> >
> > INPUT COORDINATE FILES
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md2.mdcrd.gz) is
> > an AMBER trajectory (with box info) with 398 sets
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md3.mdcrd.gz) is
> > an AMBER trajectory (with box info) with 400 sets
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md4.mdcrd.gz) is
> > an AMBER trajectory (with box info) with 400 sets
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md5.mdcrd.gz) is
> > an AMBER trajectory (with box info) with 400 sets
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md6.mdrcd.gz) is
> > an AMBER trajectory (with box info) with 400 sets
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md7.mdrcd.gz) is
> > an AMBER trajectory (with box info) with 400 sets
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md8.mdcrd.gz) is
> > an AMBER trajectory (with box info) with 400 sets
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md9.mdcrd.gz) is
> > an AMBER trajectory (with box info) with 400 sets
> > File
> > (/DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_10.mdrcd.gz) is an
> > AMBER trajectory (with box info) with 400 sets
> >
> > OUTPUT COORDINATE FILE
> > NULL entry
> >
> > ACTIONS
> > 1> RMS to first frame using no mass weighting
> > Dumping RMSd vs. time (with time interval 0.20) to a file named
> > /DATA/VINCLOZOLIN_TRAJECTORY_ANALYSIS/vinclozolin_backbone.rms
> > Atom selection follows :1-250_at_CA
> > 7> STRIP: 21090 atoms will be removed from trajectory: :252-7281
> >
> >
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md2.mdcrd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 ................................................
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md3.mdcrd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md4.mdcrd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md5.mdcrd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md6.mdrcd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md7.mdrcd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md8.mdcrd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md9.mdcrd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400
> > Processing AMBER trajectory file
> > /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_10.mdrcd.gz
> >
> > Set 1 .................................................
> > Set 50 .................................................
> > Set 100 .................................................
> > Set 150 .................................................
> > Set 200 .................................................
> > Set 250 .................................................
> > Set 300 .................................................
> > Set 350 .................................................
> > Set 400
> >
> > PTRAJ: Successfully read in 3598 sets and processed 3598 sets.
> > Dumping accumulated results (if any)
> >
> > PTRAJ RMS: dumping RMSd vs time data
> >

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• Next message: Carlos Simmerling: "Re: AMBER: RE: trouble stripping waters with ptraj"
• Previous message: Ilyas Yildirim: "Re: AMBER: Question about .off file"
• In reply to: Claire Zerafa: "AMBER: RMSd error"
• Next in thread: Claire Zerafa: "Re: AMBER: RMSd error"
• Reply: Claire Zerafa: "Re: AMBER: RMSd error"
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