AMBER Archive (2006)

Subject: AMBER: RMSd error

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Thu May 25 2006 - 23:37:54 CDT

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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