Error In Box Coord Line Of Trajectory
[ by thread ] [ by subject ] [ by author ] [ by messages with attachments ] From: Senthil Natesan Date: Mon, 10 Jun 2013 06:18:01 -0700 (PDT) Hi Dan, Yes I am using the most up-to-date version. The trajectory looks fine in VMD. I will send you the files shortly. Thanks, Senthil ________________________________ From: Daniel Roe To: Senthil Natesan ; AMBER Mailing List Sent: Friday, June 7, 2013 10:22 AM Subject: Re: [AMBER] MMPBSA.py Error Hi, Are you using the most up-to-date version of AmberTools 13? You can check by running update_amber in your $AMBERHOME directory. Remember that after patches are applied you need to recompile in order for them to take effect. Can you load the complex topology and trajectory in another program like cpptraj or VMD? It may help to track down what may be going on if you provide me (off-list) your topology files and a shorter version of your trajectory (~2 frames). -Dan On Fri, Jun 7, 2013 at 7:06 AM, Senthil Natesan wrote: > Hi Jason, > > Thanks for the suggestions. I looked at the trajectories and they seem fine. Nothing strange ! > I tried the same trajectories and inputfiles with AmberTools1.4 &Amber11 (earlier I tried the latest versions) > along with solvated complex prmtop file and it works perfectly fine (without any error) and I got the results after 8-9 hours on a single node. > > Good day ! > > Senthil > > > > > ________________________________ > From: Jason Swails > To: Senthil Natesan ; AMBER Mailing List > Sent: Thursday, June 6, 2013 11:56 AM > Subject: Re: [AMBER] MMPBSA.py Error > > > On Thu, Jun 6, 2013 at 11:46 AM, Senthil Natesan wrote: > >> Dear Amber Users, >> >> I am trying to do MMPBSA calculations with a single trajectory and gives >> the following error: >> >> ---------------------------------------------- >> >> Preparing trajectories for simulation... >> Error in box coord line of trajectory h3_820_complex_prod2.mdcrd. >> Expect only 3 or 6 box coords. >> Problem line: 4.509 71.808 82.630 27.602 29.349 36.456 58.340 >> 102.059 -20.666 >> >> Error: Could not set up h3_820_complex_prod2.mdcrd for reading. >> Error: trajin: Could not set up trajectory. >> TrajError: Trajectory h3_820_complex_prod2.mdcrd has 0 frames! >
by subject ] [ by author ] [ by messages with attachments ] From: Ray Luo, Ph.D. Date: Thu, 29 May 2014 10:01:30 -0700 Looks like something wrong with your mdcdd file. Can you visualize your files in VMD? Ray -- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Thu, May 29, 2014 at 7:03 AM, mahnam karim wrote: > > > > In God we trust > > Hello Dear Amber users: > I have done simulation http://archive.ambermd.org/201306/0233.html a protein system containing a Ca and Zn atoms and a > docked ligand. I am trying to do an MMPBSA calculation on my protein > complex. I make topologies of complex and ligand and receptor with these > commands in tleap: > tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB > addAtomTypes { > { "C0" "Ca" "sp3" } > } > loadamberparams cal.frcmod > loadoff Ca2.lib > addAtomTypes http://archive.ambermd.org/201405/0740.html { > { "Zn" "Zn" "sp3" } > } > loadamberparams zinc.frcmod > loadoff zn2.lib > REC = loadpdb a2.pdb > bond REC.170.Zn REC.83.NE2 > bond REC.170.Zn REC.68.NE2 > bond REC.170.Zn REC.96.ND1 > bond REC.169.Zn REC.122.NE2 > bond REC.169.Zn REC.118.NE2 > bond REC.169.Zn REC.128.NE2 > bond REC.171.Ca REC.75.OD1 > bond REC.171.Ca REC.80.O > bond REC.171.Ca REC.101.OE2 > bond REC.171.Ca REC.98.OD2 > charge REC > addions2 REC Na+ 0 > saveamberparm REC rec.prmtop rec.crd > loadamberprep lig.prepin > saveoff DRG lig.lib > loadamberparams lig.frcmod > loadoff lig.lib > LIG = loadpdb best2f.pdb > saveamberparm LIG lig.prmtop lig.crd > charge COM > COM = combine {REC LIG} > addions2 COM Na+ 0 > saveamberparm COM com.prmtop com.crd > ################################################################################### > > tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB > addAtomTypes { > { "C0" "Ca" "sp3" } > } > loadamberparams cal.frcmod > loadoff Ca2.lib > addAtomTypes { > { "Zn" "Zn" "sp3" } > } > loadamberparams zinc.frcmod > loadoff zn2.lib > REC = loadpdb a2.pdb > bond REC.170.Zn REC.83.NE2 > bond REC.170.Zn REC.68.NE2 > bond REC.170.Zn REC.96.ND1 > bond REC.169.Zn REC.122.NE2 > bond REC.169.Zn REC.118.NE2 > bond REC.169.Zn REC.128.NE2 > bond REC.171.Ca REC.75.OD1 > bond REC.171.Ca REC.80.O >
subject ] [ by http://archive.ambermd.org/201306/0186.html author ] [ by messages with attachments ] From: Senthil Natesan Date: Thu, 6 Jun 2013 08:46:12 -0700 (PDT) Dear Amber Users, I am trying to do MMPBSA calculations with a single trajectory and gives the following error: ---------------------------------------------- Preparing trajectories for simulation... Error in box coord line error in of trajectory h3_820_complex_prod2.mdcrd. Expect only 3 or 6 box coords. Problem line: 4.509 71.808 82.630 27.602 29.349 36.456 58.340 102.059 -20.666 Error: Could not set up h3_820_complex_prod2.mdcrd for reading. Error: trajin: Could not set up trajectory. TrajError: Trajectory h3_820_complex_prod2.mdcrd has 0 frames! Exiting. All files have been error in box retained. -------------------------------------------------- I went through the previous user lists messages, but there is no clear answers that I could find. my input file looks like this: ---------------------------------------- &general startframe=1, endframe=2500, interval=50, verbose=2, / &gb igb=5, saltcon=0.150, Earlier I prepared the input files using the following script --------------------------------------------------------- source leaprc.ff99SB loadoff aly.lib loadamberparams aly.frcmod lig = loadpdb H3_820_unmodified_ligand.pdb prot = loadpdb H3_820_unmodified_protein.pdb complex = combine{prot lig} set default PBRadii mbondi2 saveamberparm lig h3_820_lig.prmtop h3_820_lig.inpcrd saveamberparm prot h3_820_protein.prmtop h3_820_protein.inpcrd saveamberparm complex h3_820_complex.prmtop h3_820_complex.inpcrd charge complex addions complex Cl- 0 solvateOct complex TIP3PBOX 16.0 saveamberparm complex h3_820_complex_solvated.prmtop h3_820_complex_solvated.inpcrd quit ----------------------------------- I am running MMPBSA.py as follows MMPBSA.py -O -i h3820_mmpbsa.in -cp h3_820_complex.prmtop -rp h3_820_protein.prmtop -lp h3_820_lig.prmtop -y h3_820_complex_prod2.mdcrd Any suggestions would be appreciated? Thanks, Senthil Natesan _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Received on Thu Jun 06 2013 - 09:00:03 PDT This message: [ Message body ] Next m