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-- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) ------------------------------ Message: 4 Date: Thu, 20 Nov 2014 15:02:00 +0900 From: "kurisaki" <kurisaki.ncube.human.nagoya-u.ac.jp> Subject: Re: [AMBER] Pairwise vs Sander with imin=5 To: "'AMBER Mailing List'" <amber.ambermd.org> Message-ID: <000301d00487$8009db10$801d9130$.human.nagoya-u.ac.jp> Content-Type: text/plain; charset="us-ascii" Thank you for your reply, Prof. Roe, > PS - By the way, what version of cpptraj are you using? I use "CPPTRAJ: Trajectory Analysis. V14.05" > I think that 1-4 electrostatics/van der Waals terms are included for > idecomp energy decomposition 2 and 4; the 'pairwise' cpptraj command > does not calculate these, so that may be where your differences are > coming from (others who are more idecomp-savvy may want to correct me > here). The total EEL/vdW energies I get from cpptraj match sander > exactly. I also checked idecomp 3 but the difference still remained. I think 1-4 energy is cancelled when calculate inter-residue energy, Namely, energy between two independent residues such like "235-> 298" in mdout. Best regards, IK > -----Original Message----- > From: Daniel Roe [mailto:daniel.r.roe.gmail.com] > Sent: Thursday, November 20, 2014 2:14 PM > To: AMBER Mailing List > Subject: Re: [AMBER] Pairwise vs Sander with imin=5 > > Hi, > > I think that 1-4 electrostatics/van der Waals terms are included for > idecomp energy decomposition 2 and 4; the 'pairwise' cpptraj command > does not calculate these, so that may be where your differences are > coming from (others who are more idecomp-savvy may want to correct me > here). The total EEL/vdW energies I get from cpptraj match sander > exactly. > > -Dan > > PS - By the way, what version of cpptraj are you using? > > On Wed, Nov 19, 2014 at 7:01 PM, kurisaki > <kurisaki.ncube.human.nagoya-u.ac.jp> wrote: > > Dear amber developers and uses, > > > > I'm now using "pairwise" in cpptraj to > > Calculate inter-residue energy. > > > > Assuming residues A and B, > > I calculated energy three times, i.e., for A, B and A+B. > > Finally, I got inter-residue energy as Ene(A+B) - {Ene(A) + Ene(B)}. > > > > Now, I compaired the value with that obtained from sander with imin=5, > and > > idecomp = 4. > > It is "almost" a half of the "pairwise" value. > > I am assuming that "sander value" is divided by two > > To assign inter-residue energy for each residue. > > > > Is this observation right? > > > > Even so, I found the difference between sander and pairwise by ca 1 > kcal/mol, > > (for pairwise and sander, -96.6274 and -94.492 (2 x -47.246) [kcal/mol], > > respectively) > > Although I used the same value for non-bonded cutoff of value, 99 [A] for > each > > computation. > > > > Considering that each calculation is executed under the vacuum. > > This inconsistensy seems strange. > > Is there any additional difference between sander and pairwise? > > > > Thank you for your support. > > > > Best regards, > > > > Ikuo KURISAKI > > > > PS > > > > I believe "idecomp =3 or 4" does not make difference > > When inter-residue energy is calculated. > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > -- > ------------------------- > Daniel R. Roe, PhD > Department of Medicinal Chemistry > University of Utah > 30 South 2000 East, Room 307 > Salt Lake City, UT 84112-5820 > http://home.chpc.utah.edu/~cheatham/ > (801) 587-9652 > (801) 585-6208 (Fax) > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 5 Date: Thu, 20 Nov 2014 06:18:25 +0000 From: Abhishek TYAGI <atyagiaa.connect.ust.hk> Subject: [AMBER] Error in CHAMBER output To: "amber.ambermd.org" <amber.ambermd.org> Message-ID: <1416464313903.29732.connect.ust.hk> Content-Type: text/plain; charset="iso-8859-1" Hello AMBER People, I am using AMBERTOOL 14. The problem in CHAMBER to convert psf and pdb file to AMBER acceptable files, I have done following approach: My system is composed of first molecule-dna-water and file name is "ionized" A). When I tried following command: the first.inp and first.prm are parameter for first molecule. 1. $AMBERHOME/home/cbme/amber14/bin/chamber -top top_first.inp -top top_all36_na.rtf -param par_all27_first.prm -param par_all36_na.prm -xpsf ionized.psf -crd ionized.pdb -p 3.prmtop -inpcrd 3.inpcrd -nocmap Output: <get_atom_parameters>ERROR atom with mass 1 has type alreadydesignated as non-hydrogen type <get_atom_parameters> atom 4585 1.0080000000000000 H1 Cannot continue 2. Than I added one more file with water ions information than it appears: $AMBERHOME/home/cbme/amber14/bin/chamber -top top_first.inp -top top_all36_na.rtf -param par_all27_first.prm -param par_all36_na.prm -xpsf ionized.psf -crd ionized.pdb -p 3.prmtop -inpcrd 3.inpcrd -nocmap -top toppar_water_ions.str Output: <get_atom_parameters>ERROR atom with mass >1 has type alreadydesignated as non-hydrogen type <get_atom_parameters> atom 2 15.999400000000000 O5' Cannot continue B). When I tried for only dna the conversion is as follows: =========================================================== Created prmtop summary =========================================================== Number of bonds with hydrogen: 236 Number of bonds without hydrogen: 458 Number of angles with hydrogen: 557 Number of angles without hydrogen: 700 Number of dihedrals with hydrogen: 930 Number of dihedrals without hydrogen: 1334 =========================================================== Determining filetype of coordinate file: ssdna.pdb Assuming PDB File. <write_prmtop_header> NPHB 0 | Conversion carried out in 0.04 seconds C). When tried with my first molecule the conversion is as follows: =========================================================== Created prmtop summary =========================================================== Number of bonds with hydrogen: 0 Number of bonds without hydrogen: 5815 Number of angles with hydrogen: 0 Number of angles without hydrogen: 11454 Number of dihedrals with hydrogen: 0 Number of dihedrals without hydrogen: 22605 =========================================================== Determining filetype of coordinate file: first.pdb Assuming PDB File. <write_prmtop_header> make_exclusion_list reallocating 62976 <write_prmtop_header> NPHB 0 | Conversion carried out in 0.98 seconds D). For dry system first molecule-dna the output is as follows: =========================================================== PSF input parsing summary =========================================================== Number of PSF flags found: 1 Number of atoms found: 4583 Number of residues found: 3957 Number of bonds found: 6509 Number of angles found: 12711 Number of dihedrals found: 24429 Number of impropers found: 57 Number of donors found: 0 Number of acceptors found: 0 Number of explicit nonbonded exclusions found: 0 Number of groups found: 1 =========================================================== <get_atom_parameters> ERROR, topology file(s) ends without finding all atom types, number found: 33 needed ntypes: 34 Exiting =========================================================== The final thing I got is the first molecule and dna files are constructed but my solvated model and dry model files are not converted. I am not understanding where is the problem. I hope you understand what I want to ask, I am new to AMBER. Thanks in advance regards Abhi ------------------------------ Message: 6 Date: Wed, 19 Nov 2014 22:23:33 -0800 From: Robin Betz <robin.robinbetz.com> Subject: Re: [AMBER] Error in CHAMBER output To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAL9_cpdZJUW25WWnr83eD9T=tN9KwX4c3_Vbx5YYO0kG=uBNog.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi Abhi, Often this error message indicates that not all CHARMM parameters were provided for this molecule. In your case, you need to indicate additional parameter files with the -str option, not the -param option. Run chamber --help to get a full description of all the command line options for a complete explanation. Hope this helps, Robin On Wed, Nov 19, 2014 at 10:18 PM, Abhishek TYAGI <atyagiaa.connect.ust.hk> wrote: > Hello AMBER People, > > I am using AMBERTOOL 14. > > The problem in CHAMBER to convert psf and pdb file to AMBER acceptable > files, I have done following approach: My system is composed of first > molecule-dna-water and file name is "ionized" > > A). When I tried following command: the first.inp and first.prm are > parameter for first molecule. > > 1. $AMBERHOME/home/cbme/amber14/bin/chamber -top top_first.inp -top > top_all36_na.rtf -param par_all27_first.prm -param par_all36_na.prm -xpsf > ionized.psf -crd ionized.pdb -p 3.prmtop -inpcrd 3.inpcrd -nocmap > > Output: > <get_atom_parameters>ERROR atom with mass 1 has type alreadydesignated as > non-hydrogen type > <get_atom_parameters> atom 4585 1.0080000000000000 H1 > Cannot continue > > > 2. Than I added one more file with water ions information than it appears: > $AMBERHOME/home/cbme/amber14/bin/chamber -top top_first.inp -top > top_all36_na.rtf -param par_all27_first.prm -param par_all36_na.prm -xpsf > ionized.psf -crd ionized.pdb -p 3.prmtop -inpcrd 3.inpcrd -nocmap -top > toppar_water_ions.str > > Output: > > <get_atom_parameters>ERROR atom with mass >1 has type alreadydesignated > as non-hydrogen type > <get_atom_parameters> atom 2 15.999400000000000 O5' > Cannot continue > > B). When I tried for only dna the conversion is as follows: > > =========================================================== > Created prmtop summary > =========================================================== > > Number of bonds with hydrogen: 236 > Number of bonds without hydrogen: 458 > > Number of angles with hydrogen: 557 > Number of angles without hydrogen: 700 > > Number of dihedrals with hydrogen: 930 > Number of dihedrals without hydrogen: 1334 > =========================================================== > > Determining filetype of coordinate file: ssdna.pdb > Assuming PDB File. > > > <write_prmtop_header> NPHB 0 > | Conversion carried out in 0.04 seconds > > C). When tried with my first molecule the conversion is as follows: > > =========================================================== > Created prmtop summary > =========================================================== > > Number of bonds with hydrogen: 0 > Number of bonds without hydrogen: 5815 > > Number of angles with hydrogen: 0 > Number of angles without hydrogen: 11454 > > Number of dihedrals with hydrogen: 0 > Number of dihedrals without hydrogen: 22605 > =========================================================== > > Determining filetype of coordinate file: first.pdb > Assuming PDB File. > <write_prmtop_header> make_exclusion_list reallocating 62976 > > > <write_prmtop_header> NPHB 0 > | Conversion carried out in 0.98 seconds > > D). For dry system first molecule-dna the output is as follows: > > =========================================================== > PSF input parsing summary > =========================================================== > > Number of PSF flags found: 1 > > Number of atoms found: 4583 > Number of residues found: 3957 > > Number of bonds found: 6509 > Number of angles found: 12711 > Number of dihedrals found: 24429 > Number of impropers found: 57 > > Number of donors found: 0 > Number of acceptors found: 0 > Number of explicit nonbonded exclusions found: 0 > > Number of groups found: 1 > > =========================================================== > > <get_atom_parameters> ERROR, topology file(s) ends without finding all > atom types, > number found: 33 needed ntypes: 34 > Exiting > =========================================================== > > > > The final thing I got is the first molecule and dna files are constructed > but my solvated model and dry model files are not converted. > > I am not understanding where is the problem. > > I hope you understand what I want to ask, I am new to AMBER. > > Thanks in advance > > regards > Abhi > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 7 Date: Thu, 20 Nov 2014 12:25:27 +0530 From: ROOPALI VERMA <roopaliverma7.gmail.com> Subject: Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CANJDEknn+5DEUwYcsJXHsLkEqvcJMwDx8F-fS_w99gsP9kz5FQ.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 the filename is AmberTools12.tar.bz2 that i have downloaded and installed at the same time with amber12. yes all the updates have been applied. roopali On Wed, Nov 19, 2014 at 5:51 PM, Amihai <amihai.technion.ac.il> wrote: > > thank you for your reply, > I guess I have the latest AmberTools since I downloaded it at the same > time > I downloaded Amber14, > from the same place. The filename is AmberTools14.tar.bz2 > Amihai Silverman > Computing and Information Systems Division, Technion. > -- > > On 11/19/2014 02:08 PM, David A Case wrote: > > On Wed, Nov 19, 2014, ROOPALI VERMA wrote: > > mostly the errors are in the *.diff files of the sander_pbsa module > ...like sander_pbsa_ > delphi2 ,*sander_pbsa_radi ,* > > *sander_pbsa_frc/dbf_1/polyALA and so on.* > I have attached the necessary files, please have a look on it. > I shall be thankful for any suggestion or comments in this regard. > > Which version of AmberTools are you using? Are you sure all the updates > have > been applied? > > FWIW, these problems look innocuous. > > ...dac > > > _______________________________________________ > AMBER mailing list > [1]AMBER.ambermd.org > [2]http://lists.ambermd.org/mailman/listinfo/amber > > References > > 1. mailto:AMBER.ambermd.org > 2. http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 8 Date: Wed, 19 Nov 2014 21:39:51 -0800 From: Ross Walker <ross.rosswalker.co.uk> Subject: [AMBER] Reminder: NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open. To: AMBER Mailing List <amber.ambermd.org> Cc: Rommie Amaro <ramaro.ucsd.edu>, Teri Simas <tasimas.gmail.com> Message-ID: <D092BE92.4CD1B%ross.rosswalker.co.uk> Content-Type: text/plain; charset="US-ASCII" Dear All, We are glad to announce that registration is open for the NBCR Amber Workshop 2014 that will be held at the faculty club of the University of California San Diego from the Mon 15th to Thur 18th Dec 2014. The course will be taught by Ross C. Walker and Rommie Amaro with additional instructors to be determined shortly. More info: http://nbcr.ucsd.edu/wordpress2/?page_id=4086 Please feel free to forward this announcement to all your contacts. With the best regards, The Organizing Team * Program The duration of the meeting is 4 days, from Dec 15th to 18th 2014. A provisional program is available on the workshop webpage (http://nbcr.ucsd.edu/wordpress2/?page_id=4086). Typically there will be lectures 3 to 4 hours per day, and hands-on tutorials, about 4 hours per day. There will also be 2 or 3 guest research lectures from local faculty as well as a poster session in which attendees will have the opportunity to present their work and engage directly with developers of the AMBER software. Thanks to sponsorship from NVIDIA a K40 GPU will be given as a poster prize. The content of the Workshop will include: * Molecular Dynamics with Amber * Using VMD to visualize AMBER * Dealing with non-standard residues * Building protein-ligand complexes * Statistical Mechanics for Free Energy Calculations * MM/PBSA calculations * Thermodynamic Integration * Enhanced sampling techniques * Markov State Models with AMBER * Accelerated Molecular Dynamics * Using the Kepler Bioworkbench - Workflows for AMBER * Analyzing Simulations * Lipid Simulations with AMBER The target audience is graduate students and postdocs as well as a few faculty interested in learning about Molecular Dynamics techniques. The course is designed to introduce Molecular Dynamics techniques from an introductory perspective but will progress quickly. Some experience with the Linux operating system is essential but experience with AMBER or other molecular dynamics packages is not required. * Registration Registration is limited to 40 participants. The registration fee is $350 and includes a USB drive for all participants containing lecture notes, hands on tutorials and a Virtual Box image with all software used in the workshop; Coffee, snacks and refreshments on all 4 days; A buffet lunch on all 4 days; a poster session and social reception and a workshop dinner. To register please visit the following page: http://nbcr.ucsd.edu/wordpress2/?page_id=4086 Important: Registration deadline is December 1st 2014. Hotels in San Diego at this time of year are likely to fill up fast so we recommend you make arrangements soon. Information regarding finding roommates to share hotel rooms will be available during registration. Attendees are expected to bring their own laptop. The organization will provide a pen-drive with all necessary software and training material. ------------------------------ Message: 9 Date: Thu, 20 Nov 2014 11:32:49 +0100 (CET) From: Aixiao Li <li.ibpc.fr> Subject: [AMBER] adQM/MM vlimit exceeded problem To: AMBER Mailing List <amber.ambermd.org> Message-ID: <995622416.10953669.1416479569242.JavaMail.zimbra.ibpc.fr> Content-Type: text/plain; charset=utf-8 Hi, I am working on a system that bulk solvent participates directly in a proton transfer reaction. So the adaptive solvent QM/MM is a perfect solution. My goal is to run umbrella sampling with adQM/MM and do potential of mean force (PMF) study. So basically the whole story is adQM/MM umbrella sampling with nmr constraints on "O" (from my reactant) and "H" (from one bulk water) distance, let us say, windows from 2.0 ang to 1.0 ang. But while running simulations, as I define my reactant+7H2Os as my A region (with one H2O as my proton donor candidate) and 5 waters in the T region, the simulation behaves well for several time steps, but sometimes it appears "vlimit exceeded for step..." and the calculations keep going on. And the calculation could stop with error message like: "Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITER, NIT, LL, I and J are : 0 4 20 80 78 Note: This is usually a symptom of some deeper problem with the energetics of the system. Is this because that my T region is not big enough or too big? I checked the configuration with VMD, and I could not find out anything strange, there is no hydroxide or hydronium ions formed... thank you very much best ------------------------------ Message: 10 Date: Thu, 20 Nov 2014 11:15:31 -0500 From: David A Case <case.biomaps.rutgers.edu> Subject: [AMBER] Problems with AmberTools test suite To: amber.ambermd.org Message-ID: <20141120161531.GA6848.biomaps.rutgers.edu> Content-Type: text/plain; charset=us-ascii Amihai wrote: > Date: Wed, 19 Nov 2014 14:21:25 +0200 > > thank you for your reply, > I guess I have the latest AmberTools since I downloaded it at the same time > I downloaded Amber14, > from the same place. The filename is AmberTools14.tar.bz2 > Amihai Silverman > Computing and Information Systems Division, Technion. > -- > On 11/19/2014 02:08 PM, David A Case wrote: > On Wed, Nov 19, 2014, ROOPALI VERMA wrote: > mostly the errors are in the *.diff files of the sander_pbsa module > ...like sander_pbsa_ > delphi2 ,*sander_pbsa_radi ,* > *sander_pbsa_frc/dbf_1/polyALA and so on.* > I have attached the necessary files, please have a look on it. > I shall be thankful for any suggestion or comments in this regard. > Which version of AmberTools are you using? Are you sure all the updates have > been applied? > FWIW, these problems look innocuous. > ...dac It looks like two separate email threads have been combined into one. The original one (From ROOPALI VERMA) dealt with PBSA errors arising in an amber12 installation. (My best guess there: install AmberTools13 on top of your AmberTools12, i.e. in the amber12 directory, apply updates, and try again. Better, update to AmberTools14 if you can.) A second thread (from Amihai) has to do with problems arising in amber14. Unfortunately, I've lost track of what the original problem was. I'm not sure how this happened. Please don't reply to an existing message if it is not on the same subject (if that is indeed what happened.) ...dac ------------------------------ Message: 11 Date: Thu, 20 Nov 2014 12:45:08 -0500 From: Bob Healey <healer.rpi.edu> Subject: [AMBER] Errors compiling Amber 14 after applying update 7 To: amber.ambermd.org Message-ID: <546E28A4.6010600.rpi.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Just got my Amber license this week, unpacked everything and started compiling according to the manual. The first pass through (./configure gnu && make install) applied up to update 6. When I went to do the MPI build, the update script found update 7. After applying it, I can not get the compilation to complete. I even deleted my source tree and started over a few times. Before I roll back to update 6, I was wondering if anyone on this list had any advice for me. I am using Fedora 19, with stock compilers. Thank you. gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -I/usr/local/amber/amber14/include -c shake.F90 shake.F90:940.132: tected in equilibrium bond length for',/5x,'SHAKEn TI atoms',1x,i8,2x,i8,2x 1 Error: Unexpected end of format string in format string at (1) shake.F90:941.132: nchronized from V0. ',/1x,'Consider using noshake mask or disabling SHAKE.' 1 Error: Unexpected end of format string in format string at (1) shake.F90:932.41: if (master) write (mdout, 1111) abs(partner_req - req), i,j,ipartner 1 Error: FORMAT label 1111 at (1) not defined shake.F90:937.49: if (master .and. write_msg) write(mdout, 1112) 1 Error: FORMAT label 1112 at (1) not defined make[3]: *** [shake.o] Error 1 make[3]: Leaving directory `/usr/local/amber/amber14/src/pmemd/src' make[2]: *** [serial] Error 2 make[2]: Leaving directory `/usr/local/amber/amber14/src/pmemd' make[1]: *** [serial] Error 2 make[1]: Leaving directory `/usr/local/amber/amber14/src' make: *** [install] Error 2 [root.pleiades amber14]# gcc -V gcc: error: unrecognized command line option ???-V??? gcc: fatal error: no input files compilation terminated. [root.pleiades amber14]# gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.3/lto-wrapper Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-isl=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/cloog-install --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.3 20140911 (Red Hat 4.8.3-7) (GCC) -- Bob Healey Systems Administrator Biocomputation and Bioinformatics Constellation and Molecularium healer.rpi.edu (518) 276-4407 ------------------------------ Message: 12 Date: Thu, 20 Nov 2014 11:01:58 -0700 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] Pairwise vs Sander with imin=5 To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOZjS+DWuKZnC2mK3M7VRQAwYYhViAAfDCG2er9v_Dt1Wg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi, After running several tests I think I may know what is going on here. Were you calculating residue interaction energy within a single molecule? When I do pairwise decomposition with sander, idecomp 3 results are the same as idecomp 4 results if I'm only looking at residue pairwise interactions for a single molecule. What's more, it seems that 1-4 van der Waals and electrostatics are added to the total van der Waals and electrostatics no matter what. Here is an example of a single molecule with two residues: SANDER IDECOMP3: resid1 ->resid2 |internal |vdw |eel |pol |sas ====================================================================== TDC 1-> 1 0.000 0.164 -19.266 -89.941 0.000 TDC 1-> 2 0.000 0.089 -6.803 -0.741 0.000 TDC 2-> 1 0.000 0.089 -6.803 -0.741 0.000 TDC 2-> 2 0.000 2.073 27.719 -16.849 0.000 CPPTRAJ (using a development command that calculates energy, but the vdW/elec results are identical to 'pairwise'): #Frame dEvdw141.2 dEelec141.2 dEvdw1.2 dEelec1.2 ide4_V1.2 ide4_E1.2 1 0.567 3.741 -0.478 -10.543 0.089 -6.803 The columns after #Frame are delta 1-4 vdW energy, delta 1-4 elec energy, delta vdW energy, delta elec energy, sum of delta 1-4 vdW and delta vdW energies, and sum of delta 1-4 elec + delta elec energies. To match sander where the energies are split between residues, the delta here is being calculated as: (ERES1+2 - ERES1 - ERES2) / 2.0 You can see that the sander results match the cpptraj results only if the 1-4 terms are included. However, if I look at two separate molecules, each 1 residue: SANDER IDECOMP3: resid1 ->resid2 |internal |vdw |eel |pol |sas ====================================================================== TDC 1-> 1 0.000 0.164 -19.266 -95.201 0.000 TDC 1-> 2 0.000 -0.001 11.008 -10.868 0.000 TDC 2-> 1 0.000 -0.001 11.008 -10.868 0.000 TDC 2-> 2 0.000 3.874 61.173 -83.685 0.000 CPPTRAJ: #Frame dEvdw1.2 dEelec1.2 1 -0.001 11.008 Now the sander vdw/elec results match cpptraj exactly. The bottom line is that energy decomposition code in sander has a lot of bookkeeping that it does under the hood, and you have to be careful when comparing those results to the simple straightforward energy calculation in the cpptraj 'pairwise' command. Hopefully this clears things up a bit, -Dan PS - Version 14.17 of cpptraj is now available and includes many important fixes, so I recommend updating. -- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 307 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) ------------------------------ Message: 13 Date: Thu, 20 Nov 2014 20:10:08 +0200 From: Kshatresh Dutta Dubey <kshatresh.gmail.com> Subject: [AMBER] PBSA error To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAF3NQ5dscAvppWeQ9rP1irKAMFntcKKQ1hNEjGbd1q-DRXbScQ.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear Users, I am using amber 14 for pbsa program. When I am trying to run the pbsa with : pbsa -O -i pbsa.in -o pbsa.out -p ../dimer-sb-wat.prmtop -c dimer-SB-run1.rst & It is showing error: Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x2B776A0A34C7 #1 0x2B776A0A3B0E #2 0x2B776AB3463F #3 0x2B776A169990 #4 0x2B776A16A4A8 #5 0x2B776A16E2DC #6 0x4C3139 in rdparm2_ #7 0x40574F in pbsa_ ...... segmentation fault. I am using netcdf format of rst file, while my input for pbsa is : PBSA calculations input &cntrl ntx = 2, imin = 1, maxcyc = 10000, ipb = 1, inp = 0 / &pb npbverb = 1, istrng = 0, epsout = 80.0, epsin = 1.0, space = 1.0, accept = 0.00, sprob = 1.4, cutnb = 2, phiout = 1, phiform = 0 / Please help me to figure out the problem .Thanks in advance. Regards Kshatresh ------------------------------ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber End of AMBER Digest, Vol 1044, Issue 1 ************************************** _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Nov 23 2014 - 22:30:02 PST