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---- parm /home/gncp/Documents/MD/PPAR_MD_study/100ns_MD_inputfiles/2PRG_RGZ_VAC.prmtop [RGZ] trajin /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0 [RGZ] parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop [1PRG_VAC] reference 1PRG_e21.rep.c0.inpcrd parm [1PRG_VAC] [struct0] rmsd :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out 1PRG_r0_RGZ_r0.rmsd trajin /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c1 [RGZ] rmsd :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out 1PRG_r0_RGZ_r1.rmsd trajin /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0 [RGZ] reference 1PRG_e21.rep.c1.inpcrd parm [1PRG_VAC] [struct1] rmsd :1-270.CA,C,N ref [struct1] :1-270.CA,C,N out 1PRG_r1_RGZ_r0.rmsd trajin /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c1 [RGZ] rmsd :1-270.CA,C,N ref [struct1] :1-270.CA,C,N out 1PRG_r1_RGZ_r1.rmsd --------- On Mon, Dec 3, 2012 at 10:26 PM, Vaibhav Dixit <vaibhavadixit.gmail.com>wrote: > Thanks Jason, > I tried to make right input files, but could not understand the usage > given in AmberTools12 (page 193) clearly. > > I tried following input for cpptraj > > cpptraj_1PRG_RGZ_trail.in > ------------ > trajin > /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0 > parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop > reference 1PRG_e21.rep.c0.inpcrd [struct0] > rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out 1PRG_r0_RGZ_r0.rmsd > > trajin > /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c1 > parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop > reference 1PRG_e21.rep.c0.inpcrd [struct0] > rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out 1PRG_r0_RGZ_r1.rmsd > ------------ > > and got the following message from cpptraj. Please help me understand why > it could not pick the right prmtop and use only residues 1-270 for rmsd > analysis from both trajectory and reference inpcrd files. > > -------------- > linux-hb9b:/home/gncp/Documents/MD/PPAR_MD_study/1PRG/rmsd_1PRG # cpptraj > /home/gncp/Documents/MD/PPAR_MD_study/100ns_MD_inputfiles/2PRG_RGZ_VAC.prmtop > < cpptraj_1PRG_RGZ_trail.in > > CPPTRAJ: Trajectory Analysis. V12.4 > ___ ___ ___ ___ > | \/ | \/ | \/ | > _|_/\_|_/\_|_/\_|_ > > INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit: > > [trajin > /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c0] > [RGZ_e21.c0] contains 5876 frames. > > [parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop] > > [reference 1PRG_e21.rep.c0.inpcrd [struct0]] > Error: Number of atoms in Amber Restart 1PRG_e21.rep.c0.inpcrd (4401) does > not > match number in associated parmtop (4466) > Error: Could not set up 1PRG_e21.rep.c0.inpcrd for reading. > Error: reference: Could not set up trajectory. > > [rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out > 1PRG_r0_RGZ_r0.rmsd] > > [trajin > /windows/D/Users/gncp/Documents/RGZ_2cluster/RGZ_epsilon21/RGZ_e21.c1] > [RGZ_e21.c1] contains 1624 frames. > > [parm /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop] > Warning: Parm > /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop already loaded, > skipping. > > [reference 1PRG_e21.rep.c0.inpcrd [struct0]] > Error: Number of atoms in Amber Restart 1PRG_e21.rep.c0.inpcrd (4401) does > not > match number in associated parmtop (4466) > Error: Could not set up 1PRG_e21.rep.c0.inpcrd for reading. > Error: reference: Could not set up trajectory. > > [rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out > 1PRG_r0_RGZ_r1.rmsd] > > > INPUT TRAJECTORIES: > [RGZ_e21.c0] is an AMBER trajectory, Parm 0 (reading 5876 of 5876) > [RGZ_e21.c1] is an AMBER trajectory, Parm 0 (reading 1624 of 1624) > Coordinate processing will occur on 7500 frames. > > PARAMETER FILES: > 0: > /home/gncp/Documents/MD/PPAR_MD_study/100ns_MD_inputfiles/2PRG_RGZ_VAC.prmtop, > 4466 atoms, 272 res, no box, 7500 frames > 1: /home/gncp/Documents/MD/PPAR_MD_study/1PRG/1PRG_VAC.prmtop, 4401 > atoms, 270 res, no box > > REFERENCE COORDS: > No reference coordinates. > No frames defined. > > OUTPUT TRAJECTORIES: > No files. > > ACTIONS: Initializing 2 actions: > 0: [rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N out > 1PRG_r0_RGZ_r0.rmsd] > Error: Rmsd::init: Could not get reference index -1 > Error: Init failed for [rmsd BB :1-270.CA,C,N ref [struct0] :1-270.CA,C,N > out 1PRG_r0_RGZ_r0.rmsd]. > -- > > On Mon, Dec 3, 2012 at 8:23 PM, Jason Swails <jason.swails.gmail.com>wrote: > >> cpptraj was designed specifically for this task. You can load structures >> with different topologies and calculate RMSDs between 'different' >> structures (as long as the selection in both structures have the same # of >> atoms). >> >> Look at the manual for cpptraj to learn how to use it. >> >> Good luck, >> Jason >> >> On Mon, Dec 3, 2012 at 9:25 AM, Vaibhav Dixit <vaibhavadixit.gmail.com >> >wrote: >> >> > Dear Monica, >> > Waters and ions are already removed from the trajectory, so they are not >> > the source of problem here. >> > I must emphasize that, I want to plot rmsd for the trajectory with >> > reference to a structure (PDB) which has one residue less than those >> > present in the MD trajectory. >> > This is causing ptraj warning for mismatch in number of atoms. >> > >> > On Mon, Dec 3, 2012 at 6:02 PM, <monica.imtech.res.in> wrote: >> > >> > > Hi >> > > I guess ypu can remove water and other ions etc.from the prmtop file >> and >> > > then >> > > try one more time for rmsd calculation by ptraj coz atom number >> > difference >> > > can >> > > be due to this. >> > > >> > > Thanx >> > > monica >> > > >> > > >> > > > Dear Amber community members, >> > > > I have trajectory files for a protein generated from different PDB >> > files >> > > > with different number of residues. >> > > > For e.g. I have structure 1PRG with residues 1-270 and 2PRG with >> > residues >> > > > 1-271 (272 is ligand). >> > > > >> > > > Now I want to plot rmsd between trajectory of 2PRG and reference >> > > structure >> > > > (PDB generate with ambpdb) of 1PRG. >> > > > I am following the below mentioned procedure, but I'm not sure if >> the >> > > > results are meaningful (rmsd > 500 ?). Ptraj also gives warning >> that >> > > > expected and actual number of atoms are different. >> > > > >> > > > *Please suggest me how can I use two prmtop for different >> trajectories >> > > > together to get the rmsd between two trajectories of same protein >> but >> > > with >> > > > different number of residues (hence different sequence).* >> > > > >> > > > Step 1. ptraj 2PRG.prmtop < 2PRG_new_traj.in >> > > > >> > > > ptraj input file for step 1. >> > > > 2PRG_new_traj.in >> > > > ------------ >> > > > trajin 2PRG.mdcrd >> > > > strip :271 >> > > > trajout 2PRG_new.mdcrd >> > > > ----------- >> > > > >> > > > Step 2. Then I have generated prmtop for 2PRG with residue 271 >> deleted >> > > > (2PRG_new.prmtop) >> > > > >> > > > Step 3. ptraj 2PRG_new.prmtop < 2PRG_1PRG.in >> > > > >> > > > ptraj input file for step 3. >> > > > 2PRG_1PRG.in >> > > > --------- >> > > > trajin 2PRG_new.mdcrd >> > > > rms reference 1PRG.pdb out 2PRG_1PRG.rmsd :1-271.CA,C,N,O >> > > > -------- >> > > > >> > > > >> > > > -- >> > > > With regards >> > > > >> > > > Vaibhav A. Dixit >> > > > Ph.D. Scholar >> > > > Department of Medicinal Chemistry >> > > > Natl. Inst. Pharm. Edu. & Res. (NIPER) >> > > > Sector 67, Phase X, S.A.S. Nagar (Mohali) >> > > > Punjab -160 062 INDIA >> > > > Phone (Mobile): +919915214408 >> > > > E-mail: vaibhavadixit.gmail.com >> > > > www.niper.nic.in >> > > > _______________________________________________ >> > > > AMBER mailing list >> > > > AMBER.ambermd.org >> > > > http://lists.ambermd.org/mailman/listinfo/amber >> > > > >> > > >> > > >> > > ______________________________________________________________________ >> > > सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) >> > > Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF >> CSIR) >> > > सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh >> > > पिन कोड/PIN CODE :160036 >> > > दूरभाष/EPABX :0172 6665 201-202 >> > > >> > > _______________________________________________ >> > > AMBER mailing list >> > > AMBER.ambermd.org >> > > http://lists.ambermd.org/mailman/listinfo/amber >> > > >> > >> > >> > >> > -- >> > With regards >> > >> > Vaibhav A. Dixit >> > Ph.D. Scholar >> > Department of Medicinal Chemistry >> > Natl. Inst. Pharm. Edu. & Res. (NIPER) >> > Sector 67, Phase X, S.A.S. Nagar (Mohali) >> > Punjab -160 062 INDIA >> > Phone (Mobile): +919915214408 >> > E-mail: vaibhavadixit.gmail.com >> > www.niper.nic.in >> > _______________________________________________ >> > AMBER mailing list >> > AMBER.ambermd.org >> > http://lists.ambermd.org/mailman/listinfo/amber >> > >> >> >> >> -- >> Jason M. Swails >> Quantum Theory Project, >> University of Florida >> Ph.D. Candidate >> 352-392-4032 >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > With regards > > Vaibhav A. Dixit > Ph.D. Scholar > Department of Medicinal Chemistry > Natl. Inst. Pharm. Edu. & Res. (NIPER) > Sector 67, Phase X, S.A.S. Nagar (Mohali) > Punjab -160 062 INDIA > Phone (Mobile): +919915214408 > E-mail: vaibhavadixit.gmail.com > www.niper.nic.in > -- With regards Vaibhav A. Dixit Ph.D. Scholar Department of Medicinal Chemistry Natl. Inst. Pharm. Edu. & Res. (NIPER) Sector 67, Phase X, S.A.S. Nagar (Mohali) Punjab -160 062 INDIA Phone (Mobile): +919915214408 E-mail: vaibhavadixit.gmail.com www.niper.nic.in _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Dec 04 2012 - 09:30:04 PST