AMBER Archive (2006)
Subject: Re: AMBER: trouble stripping waters with ptraj
From: Asim Okur (aokur_at_ic.sunysb.edu)
Date: Tue May 16 2006 - 15:17:32 CDT
It seems like you are trying to read the stripped trajectory with
original topology file which contains waters. Try loading it with a
topology file just describing the protein without waters.
I hope this helps,
Stony Brook University
Stony Brook, NY 11794-3400
631 - 632 1560
Adam Pelzer wrote:
> Dear AMBER users,
> I am new to using ptraj, and I just tried to strip the waters from a
> trajectory file ("sim_an_1000.mdcrd") to create a new trajectory file
> without waters ("sim_an_1000_water_stripped.mdcrd"). Initially it
> seemed to work, since ptraj processed all 200 frames of the trajectory
> file without complaints. However, when I tried to use
> sim_an_1000_water_stripped.mdcrd, I was told that the the file only
> contained 30 frames, and that the 31st was corrupted:
> Processing AMBER trajectory file sim_an_1000_water_stripped
> Set 1 ..............................
> Set #31 appears corrupted (
> 49.453 27.539 40.4013)
> I am not sure whether the problem is with my input file or with the
> original trajectory file. I have cut and pasted my input file for
> stripping the waters below, as well as the output that is printed when
> I strip the waters. I would be very grateful for any suggestions on
> how to trouble-shoot this problem.
> Thank you very much in advance for any advice.
> Here's the input file:
> trajin sim_an_1000.mdcrd
> strip @5784-38092
> trajout sim_an_1000_water_stripped.mdcrd trajectory nobox
> Here's the output printed:
> Amber8 Module: ptraj
> Read in control variables
> Read in atom names...
> Read in charges...
> Read in masses...
> Read in IAC (atoms involved in L-J)...
> Read in NUMEX (index to excl atom list)...
> Read in NNO (index for nonbond of @type)...
> Read in residue labels...
> GLU THR THR ALA LEU VAL CYS ASP ASN GLY
> SER GLY LEU VAL LYS ALA GLY PHE ALA GLY
> ASP ASP ALA PRO ARG ALA VAL PHE PRO SER
> ILE VAL GLY ARG PRO ARG HIE GLN GLY VAL
> MET VAL GLY MET GLY GLN LYS ASP SER TYR
> VAL GLY ASP GLU ALA GLN SER LYS ARG GLY
> ILE LEU THR LEU LYS TYR PRO ILE GLU HIM
> GLY ILE ILE THR ASN TRP ASP ASP MET GLU
> LYS ILE TRP HID HIE THR PHE TYR ASN GLU
> LEU ARG VAL ALA PRO GLU GLU HIE PRO THR
> LEU LEU THR GLU ALA PRO LEU ASN PRO LYS
> ALA ASN ARG GLU LYS MET THR GLN ILE MET
> PHE GLU THR PHE ASN VAL PRO ALA MET TYR
> VAL ALA ILE GLN ALA VAL LEU SER LEU TYR
> ALA SER GLY ARG THR THR GLY ILE VAL LEU
> ASP SER GLY ASP GLY VAL THR HIE ASN VAL
> PRO ILE TYR GLU GLY TYR ALA LEU PRO HIE
> ALA ILE MET ARG LEU ASP LEU ALA GLY ARG
> ASP LEU THR ASP TYR LEU MET LYS ILE LEU
> THR GLU ARG GLY TYR SER PHE VAL THR THR
> ALA GLU ARG GLU ILE VAL ARG ASP ILE LYS
> GLU LYS LEU CYS TYR VAL ALA LEU ASP PHE
> GLU ASN GLU MET ALA THR ALA ALA SER SER
> SER SER LEU GLU LYS SER TYR GLU LEU PRO
> ASP GLY GLN VAL ILE THR ILE GLY ASN GLU
> ARG PHE ARG CYS PRO GLU THR LEU PHE GLN
> PRO SER PHE ILE GLY MET GLU SER ALA GLY
> ILE HIE GLU THR THR TYR ASN SER ILE MET
> LYS CYS ASP ILE ASP ILE ARG LYS ASP LEU
> TYR ALA ASN ASN VAL MET SER GLY GLY THR
> THR MET TYR PRO GLY ILE ALA ASP ARG MET
> GLN LYS GLU ILE THR ALA LEU ALA PRO SER
> THR MET LYS ILE LYS ILE ILE ALA PRO PRO
> GLU ARG LYS TYR SER VAL TRP ILE GLY GLY
> SER ILE LEU ALA SER LEU SER THR PHE GLN
> GLN MET TRP ILE THR LYS GLN GLU TYR ASP
> GLU ALA GLY PRO SER ILE VAL HIE ARG CA
> CA CA CA CA CA adp K+ K+ WAT WAT
> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
> WAT WAT WAT WAT WAT WAT WAT
> Read in the residue to atom pointer list...
> Read in bond parameters RK and REQ...
> Read in angle parameters TK and TEQ...
> Read in dihedral parameters PK, PN and PHASE...
> Read in SOLTY...
> Read in L-J parameters CN1 and CN2...
> Read in info for bonds w/ hydrogen...
> Read in info for bonds w/out hydrogen...
> Read in info for angles w/ hydrogen...
> Read in info for angles w/out hydrogen...
> Read in info for dihedrals w/ hydrogen...
> Read in info for dihedrals w/out hydrogen...
> Read in excluded atom list...
> Read in h-bond parameters: AG, BG, and HBCUT...
> Read in atomic symbols (types)...
> Read in tree information...
> Read in the JOIN info...
> Read in the IROTAT info...
> Scanning Box
> Read in box information...
> Successfully completed readParm.
> PTRAJ: Processing input file...
> Input is from standard input
> PTRAJ: trajin sim_an_1000.mdcrd
> Checking coordinates: sim_an_1000.mdcrd
> PTRAJ: center
> Mask [*] represents 38092 atoms
> PTRAJ: strip @5784-38092
> Mask [@5784-38092] represents 32309 atoms
> PTRAJ: trajout sim_an_1000_water_stripped.mdcrd trajectory nobox
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 200 frames.
> Summary of I/O and actions follows:
> INPUT COORDINATE FILES
> File (sim_an_1000.mdcrd) is an AMBER trajectory (with box info) with
> 200 sets
> OUTPUT COORDINATE FILE
> File (sim_an_1000_water_stripped.mdcrd) is an AMBER trajectory
> 1> CENTER to box center via center of geometry, atom selection
> follows * (All atoms are selected)
> 7> STRIP: 32309 atoms will be removed from trajectory: :377-11147
> Processing AMBER trajectory file sim_an_1000.mdcrd
> Set 1 .................................................
> Set 50 .................................................
> Set 100 .................................................
> Set 150 .................................................
> Set 200
> PTRAJ: Successfully read in 200 sets and processed 200 sets.
> Dumping accumulated results (if any)
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> <http://us.rd.yahoo.com/evt=40762/*http://www.yahoo.com/preview>. It's
> not radically different. Just radically better.
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