AMBER Archive (2006)

Subject: Re: AMBER: trouble stripping waters with ptraj

From: Asim Okur (
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,

Asim Okur

Asim Okur
Stony Brook University
Chemistry Department
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 > .mdcrd > > 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. > > Adam > > > Here's the input file: > > trajin sim_an_1000.mdcrd > center > 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 > > ACTIONS > 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) > > ------------------------------------------------------------------------ > Sneak preview the all-new > <*>. It's > not radically different. Just radically better.

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to