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Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ Message: 4 Date: Thu, 11 Feb 2016 12:09:15 +0530 From: Mongam Riba <mongam12.gmail.com> Subject: [AMBER] Gist Installation in Amber12 To: amber.ambermd.org Message-ID: <CAB=QPXt2sDvPwt+Rsjjng0EKsOKFa1v3QeHogHCYrB=WxpzHqA.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hello, i am a student perusing masters in bioinformatics. i am working on a protein using amber 12 package and wanted to do the GIST analysis study. but i am not able to run the gist analysis using cpptraj command. so is there a way to install gist in amber12. if there then please can you help me out i shall be very thankful to you. with regards Mongam Riba Student of Bioscienc and bioinformatics ------------------------------ Message: 5 Date: Thu, 11 Feb 2016 07:34:09 +0000 (UTC) From: Saman Yousuf ali <saman.yousufali64.yahoo.com> Subject: [AMBER] minimization error : segmentation fault To: AMBER Mailing List <amber.ambermd.org> Message-ID: <1954759321.1976941.1455176049355.JavaMail.yahoo.mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Dear all,I have tried to run minimization of apo protein. I have prepared topology files using ff14SB force field (amber14). Before running minimization, I checked my structure using cpptraj checkoverlap command to see if atoms are close to other atoms. I have found that protein contain some bad contact because leap added missing atoms then I started running minimization. I got the following error message. Sander runs for few cycles of minimization and stops with following error message (below)> minimization.inrestrain_min ?&cntrl ? imin?? = 1, ? maxcyc = 500, ? ntpr?? = 1, ? ntb??? = 1, ? cut??? = 10.0 ?/ Hold the system fixed 25.0 RES 1 541 END END > sander -O -i min1.in -p protein.prmtop -c protein.inpcrd -o protein_min1.out -r protein_min1.rst -ref protein.inpcrd > "ERROR MESSAGE" Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error: #0 0x33E3419497 #1 0x33E3419ADE #2 0x36184358EF #3 0x4D5DB5 in nb_adjust_ #4 0x4D7FE6 in ewald_force_ #5 0x64AFCF in force_ #6 0x484743 in runmin_ #7 0x47132F in sander_ #8 0x46CBBC in MAIN__ at multisander.F90:? Segmentation fault (core dumped) then I tried to minimize the same apo protein (with bad contact) via amber12 using ff99SB, minimization run perfectly with out any error message and I have completed all step then check structure again using cpptraj command. I found that after minimzation structure is fine (without any bad contacts). I used the following script for minimization, >Minimization Amber12 ?&cntrl ?imin=1, maxcyc=1000, ntmin = 2, ?ntx = 1, ntc = 1, ntf = 1, ?ntb = 1, ntp = 0, ncyc = 100, ?ntwx = 1000, ntwe = 0, ntpr = 1000, ?ntr = 1, cut = 10.0 ?&end Restraints ?25.0 RES 1 541 END END I want to know that why amber14 minimization failed while amber12 completed all minimization steps without any error message. Thank you. ?Best Regards,?Saman Yousuf AliJunior Research Fellow, | Lab No. P-133, Computational Chemistry Laboratory Dr. Panjwani Center for Molecular Medicine & Drug Research, International Center for Chemical & Biological Sciences, University of Karachi ? 75270.Karachi-Pakistan. Contact No: Office (92-21) 111222292 (Ext 309) Email ID:?saman.yousufali64.yahoo.com saman.ali.iccs.edu ?? | ------------------------------ Message: 6 Date: Wed, 10 Feb 2016 23:39:50 -0800 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] minimization error : segmentation fault To: amber.ambermd.org Message-ID: <56BC3AC6.8050301.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed Since you have ntpr=1, are any steps printed in the .out? If so, please paste a few here. Bill On 2/10/16 11:34 PM, Saman Yousuf ali wrote: > Dear all,I have tried to run minimization of apo protein. I have prepared topology files using ff14SB force field (amber14). Before running minimization, I checked my structure using cpptraj checkoverlap command to see if atoms are close to other atoms. I have found that protein contain some bad contact because leap added missing atoms then I started running minimization. I got the following error message. Sander runs for few cycles of minimization and stops with following error message (below)> minimization.inrestrain_min > &cntrl > imin = 1, > maxcyc = 500, > ntpr = 1, > ntb = 1, > cut = 10.0 > / > Hold the system fixed > 25.0 > RES 1 541 > END > END >> sander -O -i min1.in -p protein.prmtop -c protein.inpcrd -o protein_min1.out -r protein_min1.rst -ref protein.inpcrd >> "ERROR MESSAGE" > Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error: > #0 0x33E3419497 > #1 0x33E3419ADE > #2 0x36184358EF > #3 0x4D5DB5 in nb_adjust_ > #4 0x4D7FE6 in ewald_force_ > #5 0x64AFCF in force_ > #6 0x484743 in runmin_ > #7 0x47132F in sander_ > #8 0x46CBBC in MAIN__ at multisander.F90:? > Segmentation fault (core dumped) > then I tried to minimize the same apo protein (with bad contact) via amber12 using ff99SB, minimization run perfectly with out any error message and I have completed all step then check structure again using cpptraj command. I found that after minimzation structure is fine (without any bad contacts). I used the following script for minimization, >> Minimization Amber12 > &cntrl > imin=1, maxcyc=1000, ntmin = 2, > ntx = 1, ntc = 1, ntf = 1, > ntb = 1, ntp = 0, ncyc = 100, > ntwx = 1000, ntwe = 0, ntpr = 1000, > ntr = 1, cut = 10.0 > &end > Restraints > 25.0 > RES 1 541 > END > END > I want to know that why amber14 minimization failed while amber12 completed all minimization steps without any error message. > Thank you. > > > Best Regards, Saman Yousuf AliJunior Research Fellow, > | Lab No. P-133, Computational Chemistry Laboratory > Dr. Panjwani Center for Molecular Medicine & Drug Research, > International Center for Chemical & Biological Sciences, > University of Karachi ? 75270.Karachi-Pakistan. > > Contact No: > Office (92-21) 111222292 (Ext 309) > Email ID: saman.yousufali64.yahoo.com > saman.ali.iccs.edu > > | > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 7 Date: Thu, 11 Feb 2016 10:07:01 +0100 From: Karolina Markowska <markowska.kar.gmail.com> Subject: [AMBER] Is there a way to compare trajectories? To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFtT2ZxGXxaz8dqA-FPhz=GRcALv=ExmpyvF-U4por+9Lkjejg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear Amber Users, I have two simulations with the same system and I would like to compare them. Mostly I would like to check if I'm having the same protein conformations in these two simulations. Does Amber software provide a tool for that kind of analysis? I wanted to use cpptraj and use the first trajectory as reference, add the second one by trajin and calculate rmsd between them, but cpptraj uses only the first frame from that file. Can I make cpptraj to read whole trajectory as a reference? The script looked like that: parm protein.prmtop reference sim1.nc trajin sim2.nc autoimage strip :WAT strip :Na+ rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass quit | sim1.nc is the trajectory of the first simulation and sim2.nc is the trajectory from the second simulation. Thanks for your help. Best regards, Karolina Markowska PhD student ------------------------------ Message: 8 Date: Thu, 11 Feb 2016 01:19:49 -0800 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Is there a way to compare trajectories? To: amber.ambermd.org Message-ID: <56BC5235.70005.cgl.ucsf.edu> Content-Type: text/plain; charset=windows-1252; format=flowed A frame-by-frame comparison of two trajectories might have value for debugging code, but I'm not sure what the meaning would be otherwise. I speak from having actually implemented this feature in an old program. I think you might do better if you can derive clusters of conformations from each trajectory and comparing those, or just compare minimized averages of the trajectories if the conformations don't change much. Bill On 2/11/16 1:07 AM, Karolina Markowska wrote: > Dear Amber Users, > > I have two simulations with the same system and I would like to compare > them. Mostly I would like to check if I'm having the same protein > conformations in these two simulations. Does Amber software provide a tool > for that kind of analysis? > > I wanted to use cpptraj and use the first trajectory as reference, add the > second one by trajin and calculate rmsd between them, but cpptraj uses only > the first frame from that file. Can I make cpptraj to read whole trajectory > as a reference? > The script looked like that: > > parm protein.prmtop > reference sim1.nc > trajin sim2.nc > autoimage > strip :WAT > strip :Na+ > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass > quit > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the > trajectory from the second simulation. > > Thanks for your help. > Best regards, > Karolina Markowska > PhD student > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 9 Date: Thu, 11 Feb 2016 10:27:03 +0100 From: "Dr. Anselm Horn" <anselm.horn.fau.de> Subject: Re: [AMBER] Is there a way to compare trajectories? To: AMBER Mailing List <amber.ambermd.org> Message-ID: <56BC53E7.5070100.fau.de> Content-Type: text/plain; charset=ISO-8859-1 Dear Karolina, AFAIK a 'reference' is limited to a single structure. Reading in two trajectories in a row should be no problem for cpptraj, as you can give several trajin commands. For the comparison of the two trajectories you could then use e.g. a 2D-RMSD-plot or perform a cluster analysis on the combined trajectories with a subsequent inspection of the distribution of the cluster structures between the trajectories. Or you could monitor some other properties of interest and compare those values. Regards, Anselm Am 11.02.2016 10:07, schrieb Karolina Markowska: > Dear Amber Users, > > I have two simulations with the same system and I would like to compare > them. Mostly I would like to check if I'm having the same protein > conformations in these two simulations. Does Amber software provide a tool > for that kind of analysis? > > I wanted to use cpptraj and use the first trajectory as reference, add the > second one by trajin and calculate rmsd between them, but cpptraj uses only > the first frame from that file. Can I make cpptraj to read whole trajectory > as a reference? > The script looked like that: > > parm protein.prmtop > reference sim1.nc > trajin sim2.nc > autoimage > strip :WAT > strip :Na+ > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass > quit > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the > trajectory from the second simulation. > > Thanks for your help. > Best regards, > Karolina Markowska > PhD student > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > ------------------------------ Message: 10 Date: Thu, 11 Feb 2016 10:44:52 +0100 From: Karolina Markowska <markowska.kar.gmail.com> Subject: Re: [AMBER] Is there a way to compare trajectories? To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFtT2ZzS0kqwz3DEBwbbbo5vwP5mLEzANK1C_h=BTUSdwkrboA.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Thank you, Bill and Anselm for your advices, I think I will try the 2D-RMSD-plot first. Have a nice day! Karolina 2016-02-11 10:27 GMT+01:00 Dr. Anselm Horn <anselm.horn.fau.de>: > Dear Karolina, > > AFAIK a 'reference' is limited to a single structure. > > Reading in two trajectories in a row should be no problem for cpptraj, > as you can give several trajin commands. > For the comparison of the two trajectories you could then use e.g. a > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories > with a subsequent inspection of the distribution of the cluster > structures between the trajectories. Or you could monitor some other > properties of interest and compare those values. > > Regards, > > Anselm > > > Am 11.02.2016 10:07, schrieb Karolina Markowska: > > Dear Amber Users, > > > > I have two simulations with the same system and I would like to compare > > them. Mostly I would like to check if I'm having the same protein > > conformations in these two simulations. Does Amber software provide a > tool > > for that kind of analysis? > > > > I wanted to use cpptraj and use the first trajectory as reference, add > the > > second one by trajin and calculate rmsd between them, but cpptraj uses > only > > the first frame from that file. Can I make cpptraj to read whole > trajectory > > as a reference? > > The script looked like that: > > > > parm protein.prmtop > > reference sim1.nc > > trajin sim2.nc > > autoimage > > strip :WAT > > strip :Na+ > > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass > > quit > > > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the > > trajectory from the second simulation. > > > > Thanks for your help. > > Best regards, > > Karolina Markowska > > PhD student > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 11 Date: Thu, 11 Feb 2016 11:43:50 +0100 From: Elisa Pieri <elisa.pieri90.gmail.com> Subject: [AMBER] Restarting a heating simulation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CANYcjuZH3R0gXHxiJ9TTnXzvJTF2pS=rv3co9Kuvi7AjwSEAdg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear all, I'm heating my system, but the maximum walltime in my cluster is 1 week, that won't probably be enough. This in my current input: *Implicit solvent constant pH initial heating mdin &cntrl imin=0, irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, ntt=3, tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2, cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1, icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1, nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, VALUE1=10.0, VALUE2=300.0, / &wt TYPE='END' /* First of all..my system has 3744 atoms and I'm running pmemd on 36 cores (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond, so it will take more than two weeks to finish. Is it normal? Isn't it VERY slow? Second, what do I have to change in the input file when I'll have to restart the simulation? Thanks, Elisa ------------------------------ Message: 12 Date: Thu, 11 Feb 2016 16:15:44 +0530 From: neha chaudhary <nehachaudhary769.gmail.com> Subject: Re: [AMBER] Regarding MMGBSA calculation To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org> Message-ID: <CANRroAEFZc7m2AaV0emOwjP-9vP82NH+pr2xYUykhSkSjZup6A.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hello Sir, I tried the command in server as /share/apps/amber/amber12/bin/cpptraj, Fatal Error: This program was not built to run in your system. Someone else installed the program on the server. Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, On Sat, Feb 6, 2016 at 6:54 PM, David A Case <david.case.rutgers.edu> wrote: > On Sat, Feb 06, 2016, neha chaudhary wrote: > > > > I am using amber on a server, when I am runnung > /share/apps/amber/amber12/ > > bin/cpptraj, Fatal Error: This program was not built to run in your > system. > > Please verify that both the operating system and the processor support > > Intel(R) AVX. > > Did you try any of the advice that Jason or I gave to your last email? (My > response is given below.) Did you install Amber yourself, or did someone > else > do it? > > ...dac > > > > > > > What happens if you type "/share/apps/amber/amber12/bin/cpptraj" at a > > > console prompt? Do the Amber test cases mostly pass? > > > > > > Related question, especially if you get failures from the previous > > > questions: > > > what OS and compiler are you using? what arguments did you give to > Amber's > > > configure script? > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 13 Date: Thu, 11 Feb 2016 06:15:39 -0500 From: Carlos Simmerling <carlos.simmerling.gmail.com> Subject: Re: [AMBER] Is there a way to compare trajectories? To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAGk3s-RNboftknaV4r0t87jLW0V6sRur+CYvEJ2GY2swXN-v2g.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 We frequently read in 2 trajectories then do cluster analysis, and compare the population of each cluster in trajectory 1 vs 2.this gives you error bars on the population of each cluster. It's similar to 2drmsd but gives you something more quantitative. On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote: > Dear Karolina, > > AFAIK a 'reference' is limited to a single structure. > > Reading in two trajectories in a row should be no problem for cpptraj, > as you can give several trajin commands. > For the comparison of the two trajectories you could then use e.g. a > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories > with a subsequent inspection of the distribution of the cluster > structures between the trajectories. Or you could monitor some other > properties of interest and compare those values. > > Regards, > > Anselm > > > Am 11.02.2016 10:07, schrieb Karolina Markowska: > > Dear Amber Users, > > > > I have two simulations with the same system and I would like to compare > > them. Mostly I would like to check if I'm having the same protein > > conformations in these two simulations. Does Amber software provide a > tool > > for that kind of analysis? > > > > I wanted to use cpptraj and use the first trajectory as reference, add > the > > second one by trajin and calculate rmsd between them, but cpptraj uses > only > > the first frame from that file. Can I make cpptraj to read whole > trajectory > > as a reference? > > The script looked like that: > > > > parm protein.prmtop > > reference sim1.nc > > trajin sim2.nc > > autoimage > > strip :WAT > > strip :Na+ > > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass > > quit > > > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the > > trajectory from the second simulation. > > > > Thanks for your help. > > Best regards, > > Karolina Markowska > > PhD student > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 14 Date: Thu, 11 Feb 2016 12:27:46 +0100 From: Karolina Markowska <markowska.kar.gmail.com> Subject: Re: [AMBER] Is there a way to compare trajectories? To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFtT2ZyLiRKmKgXdGcd3+WZ15vGZ7O+eHD0B9U7tDs9r0pB25w.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Thank you, Carlos, that's even better! Karolina 2016-02-11 12:15 GMT+01:00 Carlos Simmerling <carlos.simmerling.gmail.com>: > We frequently read in 2 trajectories then do cluster analysis, and compare > the population of each cluster in trajectory 1 vs 2.this gives you error > bars on the population of each cluster. It's similar to 2drmsd but gives > you something more quantitative. > On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote: > > > Dear Karolina, > > > > AFAIK a 'reference' is limited to a single structure. > > > > Reading in two trajectories in a row should be no problem for cpptraj, > > as you can give several trajin commands. > > For the comparison of the two trajectories you could then use e.g. a > > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories > > with a subsequent inspection of the distribution of the cluster > > structures between the trajectories. Or you could monitor some other > > properties of interest and compare those values. > > > > Regards, > > > > Anselm > > > > > > Am 11.02.2016 10:07, schrieb Karolina Markowska: > > > Dear Amber Users, > > > > > > I have two simulations with the same system and I would like to compare > > > them. Mostly I would like to check if I'm having the same protein > > > conformations in these two simulations. Does Amber software provide a > > tool > > > for that kind of analysis? > > > > > > I wanted to use cpptraj and use the first trajectory as reference, add > > the > > > second one by trajin and calculate rmsd between them, but cpptraj uses > > only > > > the first frame from that file. Can I make cpptraj to read whole > > trajectory > > > as a reference? > > > The script looked like that: > > > > > > parm protein.prmtop > > > reference sim1.nc > > > trajin sim2.nc > > > autoimage > > > strip :WAT > > > strip :Na+ > > > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass > > > quit > > > > > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the > > > trajectory from the second simulation. > > > > > > Thanks for your help. > > > Best regards, > > > Karolina Markowska > > > PhD student > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 15 Date: Thu, 11 Feb 2016 11:30:50 +0000 From: Mohammed Khaled Tumbi <khaledtumbi.gmail.com> Subject: Re: [AMBER] Is there a way to compare trajectories? To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEJ44H=b37P+AyM0s34C4HOTwnqhYsVGCzQHGga-9Cs7VPmyKA.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear Markowska: For comparison of you can use pyPcazip. "" Trajectory compression with *pyPcazip* provides the gateway to a range of analysis methods that provide objective, quantitative and comparative metrics related to convergence and sampling, and the *similarity between one trajectory and another. "". * https://bitbucket.org/ramonbsc/pypcazip/overview https://pypi.python.org/pypi/pyPcazip This program can compare trajectories based on RMSD, PCA analysis. On Thu, 11 Feb 2016 at 11:16 Carlos Simmerling <carlos.simmerling.gmail.com> wrote: > We frequently read in 2 trajectories then do cluster analysis, and compare > the population of each cluster in trajectory 1 vs 2.this gives you error > bars on the population of each cluster. It's similar to 2drmsd but gives > you something more quantitative. > On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote: > > > Dear Karolina, > > > > AFAIK a 'reference' is limited to a single structure. > > > > Reading in two trajectories in a row should be no problem for cpptraj, > > as you can give several trajin commands. > > For the comparison of the two trajectories you could then use e.g. a > > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories > > with a subsequent inspection of the distribution of the cluster > > structures between the trajectories. Or you could monitor some other > > properties of interest and compare those values. > > > > Regards, > > > > Anselm > > > > > > Am 11.02.2016 10:07, schrieb Karolina Markowska: > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- -------------------------------------------------------- Tumbi Mohammed Khaled. ------------------------------ Message: 16 Date: Thu, 11 Feb 2016 21:17:03 +0900 From: David A Case <david.case.rutgers.edu> Subject: Re: [AMBER] Gist Installation in Amber12 To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20160211121703.GA9977.scarletmail.rutgers.edu> Content-Type: text/plain; charset=us-ascii On Thu, Feb 11, 2016, Mongam Riba wrote: > i am a student perusing masters in bioinformatics. i am working on a > protein using amber 12 package and wanted to do the GIST analysis study. > but i am not able to run the gist analysis using cpptraj command. so is > there a way to install gist in amber12. if there then please can you help > me out i shall be very thankful to you. The gist analysis is a part of cpptraj in AmberTools, which is freely available. You should download and install AmberTools15 (in a separate directory tree: the top of the Amber12 tree is .../amber12, whereas the top of the AmberTools15 tree will be .../amber14.) You can use the trajectories that you generate with Amber12 as input to the gist analysis in AmberTools15. ...good luck....dac ------------------------------ Message: 17 Date: Thu, 11 Feb 2016 13:36:50 +0100 From: Falko J?hnert <falko.jaehnert.biochemtech.uni-halle.de> Subject: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors To: amber.ambermd.org Message-ID: <000201d164c8$e4005980$ac010c80$.biochemtech.uni-halle.de> Content-Type: text/plain; charset="iso-8859-1" Dear Amberlings, at first, thanks a lot helping me out with my last problem ?Howto cpptraj - multiple trajin-commands in one line?. @Jean-Marc Billod: I did it your way and this works just fine! Now I?ve got a little concern about the results of my installation of Amber 14. The make test-procedure at the parallel installation level (both with 2 and 4 threads) went through without a single error, even without rounding mistakes. After that i?ve compiled Amber 14 the usual way to gather CUDA-support. Now the make test produce some rounding errors which are okay (I hope), but also errors where lines one of the compared files (*.diff) are inserted and thus produce a lot of differences. If one compares the numbers of the correctly aligned lines then everything is fine (I hope ? again with some rounding errors). To understand my problem better I attached the *log- and the *.diff-files which are shortened to display only the unclear diffs. Can I ignore this diffs safely? If not, may someone provide any information handling this problem? Thanks a lot in advance! Kind regards, Falko Jaehnert. -------------- next part -------------- A non-text attachment was scrubbed... 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Name: 2016-02-09_09-33-40_short.log Type: application/octet-stream Size: 1880 bytes Desc: not available Url : http://lists.ambermd.org/mailman/private/amber/attachments/20160211/d5fa555a/attachment-0003.obj ------------------------------ Message: 18 Date: Thu, 11 Feb 2016 21:45:22 +0900 From: David A Case <david.case.rutgers.edu> Subject: Re: [AMBER] Regarding MMGBSA calculation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20160211124522.GB9977.scarletmail.rutgers.edu> Content-Type: text/plain; charset=us-ascii On Thu, Feb 11, 2016, neha chaudhary wrote: > > I tried the command in server as /share/apps/amber/amber12/bin/cpptraj, Fatal > Error: This program was not built to run in your system. > Someone else installed the program on the server. There is no way that anyone on the list will be able to help. You should consider just installing AmberTools yourself (it is quite easy, assuming that the node on which you are compiling things is the same as the nodes on which it will be run). Otherwise, you will need to contact the person who installed the program and report the problem to that person. ....dac ------------------------------ Message: 19 Date: Thu, 11 Feb 2016 07:47:00 -0500 From: Arati Paudyal <apsilwal123.gmail.com> Subject: Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAJomNAhdXtrNdd07qgL6igJjvCRX6gEaxeE-CD4HRd=EFiHSvg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Jason, I tried a short run with AmberTools 15 and I still get the same error message. I re-ran the tutorial and it runs fine with AmberTools 15 as well. On Wed, Feb 10, 2016 at 9:15 PM, Jason Swails <jason.swails.gmail.com> wrote: > Have you tried yet with AmberTools 15? > > On Wed, Feb 10, 2016 at 6:42 PM, Arati Paudyal <apsilwal123.gmail.com> > wrote: > > > Thanks Jason, > > > > Could you please provide some details on how one might access those > hidden > > files? Is it stores in some kind of files or do we need to extract it? I > am > > kind of new here in Amber. Any help would be greatly appreciated. > > > > Also, if I email you the original PDB and prmtop files, is there anyway > you > > would have time to look at those and see if I am doing anything wrong in > > separating those two individual PDBs from the complex? I will email those > > to your gmail if it is ok with you. > > > > > > > > Thanks again for your valuable time. > > > > On Wed, Feb 10, 2016 at 12:00 PM, Jason Swails <jason.swails.gmail.com> > > wrote: > > > > > On Wed, Feb 10, 2016 at 10:53 AM, Arati Paudyal <apsilwal123.gmail.com > > > > > wrote: > > > > > > > Thanks for your reply, > > > > > > > > I will try to upgrade to Ambertools 15. But since the tutorial works > > just > > > > fine, do you think this could be any issue related to upgrade > though? I > > > > will follow your suggestion and see how this goes. > > > > > > > > > > ?We would need to see the output from cpptraj as it tried to compute > > > surface areas. There's almost certainly an error message hidden in > there > > > that will tell us what the problem is. > > > > > > HTH, > > > Jason > > > > > > -- > > > Jason M. Swails > > > BioMaPS, > > > Rutgers University > > > Postdoctoral Researcher > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 20 Date: Thu, 11 Feb 2016 07:50:09 -0500 From: Jason Swails <jason.swails.gmail.com> Subject: Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEk9e3phs6JrA_H-E1F7+yXsGSPBHV1LoK14PqKNgC4z4pPt0g.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Can you send me the prmtop files, input file, and a trajectory with ~2 to 3 frames so I can try to reproduce this? On Thu, Feb 11, 2016 at 7:47 AM, Arati Paudyal <apsilwal123.gmail.com> wrote: > Jason, > > I tried a short run with AmberTools 15 and I still get the same error > message. I re-ran the tutorial and it runs fine with AmberTools 15 as well. > > On Wed, Feb 10, 2016 at 9:15 PM, Jason Swails <jason.swails.gmail.com> > wrote: > > > Have you tried yet with AmberTools 15? > > > > On Wed, Feb 10, 2016 at 6:42 PM, Arati Paudyal <apsilwal123.gmail.com> > > wrote: > > > > > Thanks Jason, > > > > > > Could you please provide some details on how one might access those > > hidden > > > files? Is it stores in some kind of files or do we need to extract it? > I > > am > > > kind of new here in Amber. Any help would be greatly appreciated. > > > > > > Also, if I email you the original PDB and prmtop files, is there anyway > > you > > > would have time to look at those and see if I am doing anything wrong > in > > > separating those two individual PDBs from the complex? I will email > those > > > to your gmail if it is ok with you. > > > > > > > > > > > > Thanks again for your valuable time. > > > > > > On Wed, Feb 10, 2016 at 12:00 PM, Jason Swails <jason.swails.gmail.com > > > > > wrote: > > > > > > > On Wed, Feb 10, 2016 at 10:53 AM, Arati Paudyal < > apsilwal123.gmail.com > > > > > > > wrote: > > > > > > > > > Thanks for your reply, > > > > > > > > > > I will try to upgrade to Ambertools 15. But since the tutorial > works > > > just > > > > > fine, do you think this could be any issue related to upgrade > > though? I > > > > > will follow your suggestion and see how this goes. > > > > > > > > > > > > > ?We would need to see the output from cpptraj as it tried to compute > > > > surface areas. There's almost certainly an error message hidden in > > there > > > > that will tell us what the problem is. > > > > > > > > HTH, > > > > Jason > > > > > > > > -- > > > > Jason M. Swails > > > > BioMaPS, > > > > Rutgers University > > > > Postdoctoral Researcher > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > -- > > Jason M. Swails > > BioMaPS, > > Rutgers University > > Postdoctoral Researcher > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ Message: 21 Date: Thu, 11 Feb 2016 21:50:39 +0900 From: David A Case <david.case.rutgers.edu> Subject: Re: [AMBER] Restarting a heating simulation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20160211125039.GC9977.scarletmail.rutgers.edu> Content-Type: text/plain; charset=us-ascii On Thu, Feb 11, 2016, Elisa Pieri wrote: > > *Implicit solvent constant pH initial heating mdin &cntrl imin=0, > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, ntt=3, > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2, > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1, > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1, > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, VALUE1=10.0, > VALUE2=300.0, / &wt TYPE='END' /* > > First of all..my system has 3744 atoms and I'm running pmemd on 36 cores > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond, > so it will take more than two weeks to finish. Is it normal? Isn't it VERY > slow? Try reducing the cutoff (to say, 20 Ang.). Also see if lowering the number of cores makes the program go faster (depends a *lot* on the details of your machine, so it is hard to make generalizations.) Also check whether the presence of a non-zero value for icnstph is having an effect on timings. If you do the run in pieces, set ntx=5 and irest=1 when you restart, using the restart file from the first run as the input to the second run. ....dac ------------------------------ Message: 22 Date: Thu, 11 Feb 2016 08:00:24 -0500 From: Jason Swails <jason.swails.gmail.com> Subject: Re: [AMBER] Restarting a heating simulation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEk9e3qzee05O3DY-oH56Qd8UzgAwPq39NuGxUYti-N8KENXvg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On Thu, Feb 11, 2016 at 5:43 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote: > Dear all, > > I'm heating my system, but the maximum walltime in my cluster is 1 week, > that won't probably be enough. This in my current input: > > > > > > > > > > > > > > > > > > > *Implicit solvent constant pH initial heating mdin &cntrl imin=0, > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, ntt=3, > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2, > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1, > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1, > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, VALUE1=10.0, > VALUE2=300.0, / &wt TYPE='END' /* > > First of all..my system has 3744 atoms and I'm running pmemd on 36 cores > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond, > so it will take more than two weeks to finish. Is it normal? Isn't it VERY > slow? > ?How exactly are you running in parallel? (i.e., what is the exact command that you are using?) There are a number of possible issues. A common mistake people make trying to run pmemd in parallel is to use a command that looks like mpirun -np 36 pmemd -O -i mdin ... The problem here is that pmemd (and sander) are serial executables that are incapable of parallelizing their calculation. The correct thing to do is mpirun -np 36 pmemd.MPI -O -i ... If you use pmemd instead of pmemd.MPI, then you will get the exact same performance as running on 1 CPU (perhaps worse if the CPUs are oversubscribed). It's also possible if you are asking for multiple nodes that all of the threads are running on a single node (which will slow down performance substantially). You'd have to ask your help staff to figure out if that's happening (and how to fix it), though. HTH, Jason -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ Message: 23 Date: Thu, 11 Feb 2016 08:03:19 -0500 From: Jason Swails <jason.swails.gmail.com> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEk9e3pWj7TeemNVMkZvrwi2xSLSqTgnJXS2L2js9gtoh938cg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On Thu, Feb 11, 2016 at 7:36 AM, Falko J?hnert < falko.jaehnert.biochemtech.uni-halle.de> wrote: > Dear Amberlings, > > > > at first, thanks a lot helping me out with my last problem ?Howto cpptraj - > multiple trajin-commands in one line?. .Jean-Marc Billod: I did it your way > and this works just fine! > > > > Now I?ve got a little concern about the results of my installation of Amber > 14. The make test-procedure at the parallel installation level (both with 2 > and 4 threads) went through without a single error, even without rounding > mistakes. After that i?ve compiled Amber 14 the usual way to gather > CUDA-support. Now the make test produce some rounding errors which are okay > (I hope), but also errors where lines one of the compared files (*.diff) > are > inserted and thus produce a lot of differences. If one compares the numbers > of the correctly aligned lines then everything is fine (I hope ? again with > some rounding errors). To understand my problem better I attached the *log- > and the *.diff-files which are shortened to display only the unclear diffs. > > > > Can I ignore this diffs safely? If not, may someone provide any information > handling this problem? > ?This is a known deficiency in the CUDA testing infrastructure. All of the larger failures (i.e., that are not round-off) arise from stochastic methods (ntt=2 or ntt=3) where the random number stream is different on every GPU. While there is a way to fix it (and it is on the to-do list), it apparently hasn't been important enough to make it to the top yet. HTH, Jason ? -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ Message: 24 Date: Thu, 11 Feb 2016 14:05:21 +0100 From: Elisa Pieri <elisa.pieri90.gmail.com> Subject: Re: [AMBER] Restarting a heating simulation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CANYcjubYjbQZ7zUVUMgHPLw595op4EqRBkWrNoDiVwoHGeihyg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 This is the command I'm using: mpiexec -n 36 pmemd.MPI -O -i heat.mdin -c crys.min.rst7 -p crys.parm7 -cpin crys.cpin -o crys.heat.mdout -r crys.heat.rst7 -ref crys.min.rst7 -x crys.heat.nc (so I guess it's ok). I'm using 3 nodes, 12 cores each. Elisa On Thu, Feb 11, 2016 at 2:00 PM, Jason Swails <jason.swails.gmail.com> wrote: > On Thu, Feb 11, 2016 at 5:43 AM, Elisa Pieri <elisa.pieri90.gmail.com> > wrote: > > > Dear all, > > > > I'm heating my system, but the maximum walltime in my cluster is 1 week, > > that won't probably be enough. This in my current input: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *Implicit solvent constant pH initial heating mdin &cntrl imin=0, > > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, > ntt=3, > > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2, > > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1, > > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1, > > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, > VALUE1=10.0, > > VALUE2=300.0, / &wt TYPE='END' /* > > > > First of all..my system has 3744 atoms and I'm running pmemd on 36 cores > > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond, > > so it will take more than two weeks to finish. Is it normal? Isn't it > VERY > > slow? > > > > ?How exactly are you running in parallel? (i.e., what is the exact command > that you are using?) There are a number of possible issues. > > A common mistake people make trying to run pmemd in parallel is to use a > command that looks like > > mpirun -np 36 pmemd -O -i mdin ... > > The problem here is that pmemd (and sander) are serial executables that are > incapable of parallelizing their calculation. The correct thing to do is > > mpirun -np 36 pmemd.MPI -O -i ... > > If you use pmemd instead of pmemd.MPI, then you will get the exact same > performance as running on 1 CPU (perhaps worse if the CPUs are > oversubscribed). It's also possible if you are asking for multiple nodes > that all of the threads are running on a single node (which will slow down > performance substantially). You'd have to ask your help staff to figure > out if that's happening (and how to fix it), though. > > HTH, > Jason > > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 25 Date: Thu, 11 Feb 2016 08:14:29 -0500 From: Carlos Simmerling <carlos.simmerling.gmail.com> Subject: Re: [AMBER] Restarting a heating simulation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAGk3s-RXhdcbT6AMaAxZBj9_aAQU8ECKiS+xW-VGRm1cB+uODA.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 I would suggest trying on a single node first, and then seeing if using more than 1 is faster or slower. On Feb 11, 2016 8:05 AM, "Elisa Pieri" <elisa.pieri90.gmail.com> wrote: > This is the command I'm using: > > mpiexec -n 36 pmemd.MPI -O -i heat.mdin -c crys.min.rst7 -p crys.parm7 > -cpin crys.cpin -o crys.heat.mdout -r crys.heat.rst7 -ref crys.min.rst7 -x > crys.heat.nc > > (so I guess it's ok). I'm using 3 nodes, 12 cores each. > > Elisa > > On Thu, Feb 11, 2016 at 2:00 PM, Jason Swails <jason.swails.gmail.com> > wrote: > > > On Thu, Feb 11, 2016 at 5:43 AM, Elisa Pieri <elisa.pieri90.gmail.com> > > wrote: > > > > > Dear all, > > > > > > I'm heating my system, but the maximum walltime in my cluster is 1 > week, > > > that won't probably be enough. This in my current input: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *Implicit solvent constant pH initial heating mdin &cntrl imin=0, > > > irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, > > ntt=3, > > > tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2, > > > cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1, > > > icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1, > > > nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, > > VALUE1=10.0, > > > VALUE2=300.0, / &wt TYPE='END' /* > > > > > > First of all..my system has 3744 atoms and I'm running pmemd on 36 > cores > > > (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per > picosecond, > > > so it will take more than two weeks to finish. Is it normal? Isn't it > > VERY > > > slow? > > > > > > > ?How exactly are you running in parallel? (i.e., what is the exact > command > > that you are using?) There are a number of possible issues. > > > > A common mistake people make trying to run pmemd in parallel is to use a > > command that looks like > > > > mpirun -np 36 pmemd -O -i mdin ... > > > > The problem here is that pmemd (and sander) are serial executables that > are > > incapable of parallelizing their calculation. The correct thing to do is > > > > mpirun -np 36 pmemd.MPI -O -i ... > > > > If you use pmemd instead of pmemd.MPI, then you will get the exact same > > performance as running on 1 CPU (perhaps worse if the CPUs are > > oversubscribed). It's also possible if you are asking for multiple nodes > > that all of the threads are running on a single node (which will slow > down > > performance substantially). You'd have to ask your help staff to figure > > out if that's happening (and how to fix it), though. > > > > HTH, > > Jason > > > > -- > > Jason M. Swails > > BioMaPS, > > Rutgers University > > Postdoctoral Researcher > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 26 Date: Thu, 11 Feb 2016 14:37:32 +0100 From: Falko J?hnert <falko.jaehnert.biochemtech.uni-halle.de> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors To: 'AMBER Mailing List' <amber.ambermd.org> Message-ID: <001001d164d1$5eb92730$1c2b7590$.biochemtech.uni-halle.de> Content-Type: text/plain; charset=utf-8 Dear Jason, thanks a lot for the quick reply. So as it is a deficiency in the testing procedure it isn?t a problem for using Amber with CUDA, right? I'm not entirely sure if I understand your answer correctly. Where did this inserted lines in one of the compared files arise from? I believed this extra lines came from an alternative logging manner? Thanks in advance, Falko J?hnert -----Urspr?ngliche Nachricht----- Von: Jason Swails [mailto:jason.swails.gmail.com] Gesendet: Donnerstag, 11. Februar 2016 14:03 An: AMBER Mailing List <amber.ambermd.org> Betreff: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors On Thu, Feb 11, 2016 at 7:36 AM, Falko J?hnert < falko.jaehnert.biochemtech.uni-halle.de> wrote: > Dear Amberlings, > > > > at first, thanks a lot helping me out with my last problem ?Howto > cpptraj - multiple trajin-commands in one line?. @Jean-Marc Billod: I > did it your way and this works just fine! > > > > Now I?ve got a little concern about the results of my installation of > Amber 14. The make test-procedure at the parallel installation level > (both with 2 and 4 threads) went through without a single error, even > without rounding mistakes. After that i?ve compiled Amber 14 the usual > way to gather CUDA-support. Now the make test produce some rounding > errors which are okay (I hope), but also errors where lines one of the > compared files (*.diff) are inserted and thus produce a lot of > differences. If one compares the numbers of the correctly aligned > lines then everything is fine (I hope ? again with some rounding > errors). To understand my problem better I attached the *log- and the > *.diff-files which are shortened to display only the unclear diffs. > > > > Can I ignore this diffs safely? If not, may someone provide any > information handling this problem? > ?This is a known deficiency in the CUDA testing infrastructure. All of the larger failures (i.e., that are not round-off) arise from stochastic methods (ntt=2 or ntt=3) where the random number stream is different on every GPU. While there is a way to fix it (and it is on the to-do list), it apparently hasn't been important enough to make it to the top yet. HTH, Jason ? -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 27 Date: Thu, 11 Feb 2016 08:20:04 -0700 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] Is there a way to compare trajectories? To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOY9dL6f1MJznUghutOR6iYe=b8Lyp1Vnbdh_KADHf-qYQ.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Just to add a bit to what Carlos said, CPPTRAJ does this kind of combined cluster analysis natively. You just read in your two separate trajectories, and cluster on them with the 'summarysplit' and 'splitframe' keywords. For example, if you have two trajectories each with 1000 frames you could cluster like so: parm myparm.parm7 trajin traj1.nc trajin traj2.nc cluster <clustering options> summarysplit split.dat splitframe 1000 This can be used to compare any number of trajectories. Another method that we have been using to compare different trajectories is to calculate the Kullback-Leibler divergence to quantify the overlap of various distributions calculated from each trajectory - in particular the principal component projection histograms. For some examples of these kinds of calculations (as well as example cpptraj scripts) see these articles and their supporting info: http://pubs.acs.org/doi/abs/10.1021/jp4125099 http://pubs.acs.org/doi/abs/10.1021/ct400862k Hope this helps, -Dan On Thu, Feb 11, 2016 at 4:27 AM, Karolina Markowska <markowska.kar.gmail.com> wrote: > Thank you, Carlos, that's even better! > > Karolina > > 2016-02-11 12:15 GMT+01:00 Carlos Simmerling <carlos.simmerling.gmail.com>: > >> We frequently read in 2 trajectories then do cluster analysis, and compare >> the population of each cluster in trajectory 1 vs 2.this gives you error >> bars on the population of each cluster. It's similar to 2drmsd but gives >> you something more quantitative. >> On Feb 11, 2016 4:27 AM, "Dr. Anselm Horn" <anselm.horn.fau.de> wrote: >> >> > Dear Karolina, >> > >> > AFAIK a 'reference' is limited to a single structure. >> > >> > Reading in two trajectories in a row should be no problem for cpptraj, >> > as you can give several trajin commands. >> > For the comparison of the two trajectories you could then use e.g. a >> > 2D-RMSD-plot or perform a cluster analysis on the combined trajectories >> > with a subsequent inspection of the distribution of the cluster >> > structures between the trajectories. Or you could monitor some other >> > properties of interest and compare those values. >> > >> > Regards, >> > >> > Anselm >> > >> > >> > Am 11.02.2016 10:07, schrieb Karolina Markowska: >> > > Dear Amber Users, >> > > >> > > I have two simulations with the same system and I would like to compare >> > > them. Mostly I would like to check if I'm having the same protein >> > > conformations in these two simulations. Does Amber software provide a >> > tool >> > > for that kind of analysis? >> > > >> > > I wanted to use cpptraj and use the first trajectory as reference, add >> > the >> > > second one by trajin and calculate rmsd between them, but cpptraj uses >> > only >> > > the first frame from that file. Can I make cpptraj to read whole >> > trajectory >> > > as a reference? >> > > The script looked like that: >> > > >> > > parm protein.prmtop >> > > reference sim1.nc >> > > trajin sim2.nc >> > > autoimage >> > > strip :WAT >> > > strip :Na+ >> > > rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass >> > > quit >> > > >> > > | sim1.nc is the trajectory of the first simulation and sim2.nc is the >> > > trajectory from the second simulation. >> > > >> > > Thanks for your help. >> > > Best regards, >> > > Karolina Markowska >> > > PhD student >> > > _______________________________________________ >> > > AMBER mailing list >> > > AMBER.ambermd.org >> > > http://lists.ambermd.org/mailman/listinfo/amber >> > > >> > > >> > >> > >> > _______________________________________________ >> > AMBER mailing list >> > AMBER.ambermd.org >> > http://lists.ambermd.org/mailman/listinfo/amber >> > >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > 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) ------------------------------ Message: 28 Date: Thu, 11 Feb 2016 08:22:49 -0700 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] Regarding MMGBSA calculation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOYbSZ3OJd4szu-Gu5QzjmW-SawtQhXY3cEzszjjQ=2XWg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 I've seen this kind of error pop up on heterogeneous clusters with Intel compilers due to the aggressive CPU-specific optimizations they employ. If you want programs to be transferable between different machines in such an environment you may have some luck configuring with the '-nosse' flag. Otherwise just take Dave's advice and compile your own local AmberTools. -Dan On Thu, Feb 11, 2016 at 3:45 AM, neha chaudhary <nehachaudhary769.gmail.com> wrote: > Hello Sir, > > I tried the command in server as /share/apps/amber/amber12/bin/cpptraj, Fatal > Error: This program was not built to run in your system. > Someone else installed the program on the server. > > Best Regards, > > *Neha* > > Research Scholar, > Centre for Computational Biology and Bioinformatics, > School of Life Sciences, > Central University of Himachal Pradesh, > > > > > > On Sat, Feb 6, 2016 at 6:54 PM, David A Case <david.case.rutgers.edu> wrote: > >> On Sat, Feb 06, 2016, neha chaudhary wrote: >> > >> > I am using amber on a server, when I am runnung >> /share/apps/amber/amber12/ >> > bin/cpptraj, Fatal Error: This program was not built to run in your >> system. >> > Please verify that both the operating system and the processor support >> > Intel(R) AVX. >> >> Did you try any of the advice that Jason or I gave to your last email? (My >> response is given below.) Did you install Amber yourself, or did someone >> else >> do it? >> >> ...dac >> >> > > >> > > What happens if you type "/share/apps/amber/amber12/bin/cpptraj" at a >> > > console prompt? Do the Amber test cases mostly pass? >> > > >> > > Related question, especially if you get failures from the previous >> > > questions: >> > > what OS and compiler are you using? what arguments did you give to >> Amber's >> > > configure script? >> > > >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > 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) ------------------------------ Message: 29 Date: Thu, 11 Feb 2016 07:29:26 -0800 From: Ross Walker <ross.rosswalker.co.uk> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors To: AMBER Mailing List <amber.ambermd.org> Message-ID: <A344F081-1114-425B-ABA6-3F4058F32EB5.rosswalker.co.uk> Content-Type: text/plain; charset=utf-8 FYI This will be fixed in AMBER 16. For now if you are concerned you can build the DPFP model and test that: ./configure -cuda_DPFP gnu make install cd test ./test_amber_cuda.sh DPFP The only difference here is the precision model so you get less rounding (the rest of the code is identical) so this will give you a valid test of whether things are working or not. Ultimately our test cases on the user pespective are way too complicated. The test suite is really designed as regression tests for those modifying the code etc while what an end user test cases need to be is one that just checks the compilation worked and tests a reasonable range of options to look for obvious compiler bugs etc. Unfortunately nobody has volunteered yet to split the testing in this way so users run the very long and complicated regression test which can lead to confusion. TLNR you are fine - the issue is rounding differences on different hardware - it's tricky to deal with with Newtonian integrators but the AMBER 16 approach should be more robust. > On Feb 11, 2016, at 05:03, Jason Swails <jason.swails.gmail.com> wrote: > > On Thu, Feb 11, 2016 at 7:36 AM, Falko J?hnert < > falko.jaehnert.biochemtech.uni-halle.de> wrote: > >> Dear Amberlings, >> >> >> >> at first, thanks a lot helping me out with my last problem ?Howto cpptraj - >> multiple trajin-commands in one line?. @Jean-Marc Billod: I did it your way >> and this works just fine! >> >> >> >> Now I?ve got a little concern about the results of my installation of Amber >> 14. The make test-procedure at the parallel installation level (both with 2 >> and 4 threads) went through without a single error, even without rounding >> mistakes. After that i?ve compiled Amber 14 the usual way to gather >> CUDA-support. Now the make test produce some rounding errors which are okay >> (I hope), but also errors where lines one of the compared files (*.diff) >> are >> inserted and thus produce a lot of differences. If one compares the numbers >> of the correctly aligned lines then everything is fine (I hope ? again with >> some rounding errors). To understand my problem better I attached the *log- >> and the *.diff-files which are shortened to display only the unclear diffs. >> >> >> >> Can I ignore this diffs safely? If not, may someone provide any information >> handling this problem? >> > > ?This is a known deficiency in the CUDA testing infrastructure. All of the > larger failures (i.e., that are not round-off) arise from stochastic > methods (ntt=2 or ntt=3) where the random number stream is different on > every GPU. > > While there is a way to fix it (and it is on the to-do list), it apparently > hasn't been important enough to make it to the top yet. > > HTH, > Jason > ? > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 30 Date: Thu, 11 Feb 2016 07:31:54 -0800 From: Ross Walker <ross.rosswalker.co.uk> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors To: AMBER Mailing List <amber.ambermd.org> Message-ID: <FC344A9B-F62B-4F5D-9358-D8C1183644AD.rosswalker.co.uk> Content-Type: text/plain; charset=utf-8 Actually, looking more closely, the main failures shown here are all for IGB=8. This is because update.12 changed the GBNeck2 parameters and thus all IGB=8 results: http://ambermd.org/bugfixes/14.0/update.12 It did not however update the test cases. So in this case the test suite is correct - IGB8 is now, as far as the test suite is concerned, giving incorrect answers. The IGB8 test output needs to be updated and the author of update.12 should make an additional update to fix this. All the best Ross > On Feb 11, 2016, at 05:03, Jason Swails <jason.swails.gmail.com> wrote: > > On Thu, Feb 11, 2016 at 7:36 AM, Falko J?hnert < > falko.jaehnert.biochemtech.uni-halle.de> wrote: > >> Dear Amberlings, >> >> >> >> at first, thanks a lot helping me out with my last problem ?Howto cpptraj - >> multiple trajin-commands in one line?. @Jean-Marc Billod: I did it your way >> and this works just fine! >> >> >> >> Now I?ve got a little concern about the results of my installation of Amber >> 14. The make test-procedure at the parallel installation level (both with 2 >> and 4 threads) went through without a single error, even without rounding >> mistakes. After that i?ve compiled Amber 14 the usual way to gather >> CUDA-support. Now the make test produce some rounding errors which are okay >> (I hope), but also errors where lines one of the compared files (*.diff) >> are >> inserted and thus produce a lot of differences. If one compares the numbers >> of the correctly aligned lines then everything is fine (I hope ? again with >> some rounding errors). To understand my problem better I attached the *log- >> and the *.diff-files which are shortened to display only the unclear diffs. >> >> >> >> Can I ignore this diffs safely? If not, may someone provide any information >> handling this problem? >> > > ?This is a known deficiency in the CUDA testing infrastructure. All of the > larger failures (i.e., that are not round-off) arise from stochastic > methods (ntt=2 or ntt=3) where the random number stream is different on > every GPU. > > While there is a way to fix it (and it is on the to-do list), it apparently > hasn't been important enough to make it to the top yet. > > HTH, > Jason > ? > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 31 Date: Thu, 11 Feb 2016 15:34:56 +0000 From: "Aronica, Pietro" <pietro.aronica07.imperial.ac.uk> Subject: [AMBER] Quasi-harmonic Calculations To: AMBER Mailing List <amber.ambermd.org> Message-ID: <VI1PR06MB1037CFA215F53FCA655084D4A4A80.VI1PR06MB1037.eurprd06.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Hello, I wanted to perform quasi-harmonic calculations of an interaction I have to estimate the entropy. I have been told that in order for this to work properly, the simulation needs to be of at least a certain length. I've also been told that this issue had been discussed on the mailing list before, but I have failed to find relevant information, just hints, and the tutorials are rather vague on the subject. Where can I find exact information on how quasi-harmonic calculations ought to be run? Cheers Pietro ------------------------------ Message: 32 Date: Thu, 11 Feb 2016 15:40:50 +0000 From: "Osman, Roman" <roman.osman.mssm.edu> Subject: Re: [AMBER] Is there a way to compare trajectories? To: AMBER Mailing List <amber.ambermd.org> Message-ID: <251B001D-4C01-4DBB-98D8-83D9B158C37B.mssm.edu> Content-Type: text/plain; charset="us-ascii" Karolyn's My colleague Mihaly Mezei implemented a 2D rmsd comparison of two trajectories. Please contact him. Mihaly.mezei.mssm.edu I used it and it's a great tool Roman Osman Sent from my iPhone > On Feb 11, 2016, at 4:45 AM, Karolina Markowska <markowska.kar.gmail.com> wrote: > > Thank you, Bill and Anselm for your advices, > > I think I will try the 2D-RMSD-plot first. > > Have a nice day! > Karolina > > 2016-02-11 10:27 GMT+01:00 Dr. Anselm Horn <anselm.horn.fau.de>: > >> Dear Karolina, >> >> AFAIK a 'reference' is limited to a single structure. >> >> Reading in two trajectories in a row should be no problem for cpptraj, >> as you can give several trajin commands. >> For the comparison of the two trajectories you could then use e.g. a >> 2D-RMSD-plot or perform a cluster analysis on the combined trajectories >> with a subsequent inspection of the distribution of the cluster >> structures between the trajectories. Or you could monitor some other >> properties of interest and compare those values. >> >> Regards, >> >> Anselm >> >> >> Am 11.02.2016 10:07, schrieb Karolina Markowska: >>> Dear Amber Users, >>> >>> I have two simulations with the same system and I would like to compare >>> them. Mostly I would like to check if I'm having the same protein >>> conformations in these two simulations. Does Amber software provide a >> tool >>> for that kind of analysis? >>> >>> I wanted to use cpptraj and use the first trajectory as reference, add >> the >>> second one by trajin and calculate rmsd between them, but cpptraj uses >> only >>> the first frame from that file. Can I make cpptraj to read whole >> trajectory >>> as a reference? >>> The script looked like that: >>> >>> parm protein.prmtop >>> reference sim1.nc >>> trajin sim2.nc >>> autoimage >>> strip :WAT >>> strip :Na+ >>> rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass >>> quit >>> >>> | sim1.nc is the trajectory of the first simulation and sim2.nc is the >>> trajectory from the second simulation. >>> >>> Thanks for your help. >>> Best regards, >>> Karolina Markowska >>> PhD student >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e= >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e= > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e= ------------------------------ Message: 33 Date: Thu, 11 Feb 2016 11:04:12 -0500 From: Jason Swails <jason.swails.gmail.com> Subject: Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEk9e3q2pOm-OJxZ6763Tx6uE0fH6ONby-uR=KBatbKk0M=ofA.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On Thu, Feb 11, 2016 at 10:31 AM, Ross Walker <ross.rosswalker.co.uk> wrote: > Actually, looking more closely, the main failures shown here are all for > IGB=8. This is because update.12 changed the GBNeck2 parameters and thus > all IGB=8 results: > > http://ambermd.org/bugfixes/14.0/update.12 > > It did not however update the test cases. So in this case the test suite > is correct - IGB8 is now, as far as the test suite is concerned, giving > incorrect answers. The IGB8 test output needs to be updated and the author > of update.12 should make an additional update to fix this. > ?The results are the same, but the output info in the header is mismatched. But since I fixed all your Makefile stuff with pmemd.cuda, I'll let you handle the CUDA test update if you want it fixed ;). -Jason ? -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ Message: 34 Date: Thu, 11 Feb 2016 11:42:57 -0500 From: Jason Swails <jason.swails.gmail.com> Subject: Re: [AMBER] Quasi-harmonic Calculations To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEk9e3pc9xJ2ZtCSSQa7EPoZeyV+8=uxUb4Wti9+8P8zO83osQ.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On Thu, Feb 11, 2016 at 10:34 AM, Aronica, Pietro < pietro.aronica07.imperial.ac.uk> wrote: > Hello, > I wanted to perform quasi-harmonic calculations of an interaction I have > to estimate the entropy. I have been told that in order for this to work > properly, the simulation needs to be of at least a certain length. I've > also been told that this issue had been discussed on the mailing list > before, but I have failed to find relevant information, just hints, and the > tutorials are rather vague on the subject. Where can I find exact > information on how quasi-harmonic calculations ought to be run? > ?Journal articles. There seem to be some promising hits on Google Scholar: https://scholar.google.com/scholar?hl=en&q=quasi-harmonic+entropy&btnG=&as_sdt=1%2C5&as_sdtp= It may also take some amount of "try it and see" (e.g., in terms of how many frames to include, etc.). HTH, Jason -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher ------------------------------ Message: 35 Date: Thu, 11 Feb 2016 11:57:39 -0500 From: kaushik chakraborty <kaushik290187.gmail.com> Subject: [AMBER] Unable to run QM/MM with RNA and sodium ion To: amber.ambermd.org Message-ID: <CAK=ChW93K5LYMsxM+y35KKf22jCruGiE-ALBjQ6Mfkv-OhvgVw.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear All, I was trying to perform qm/mm simulation of a RNA molecule using CHARMM forcefield in amber 12. It was running fine when I there is only RNA atoms within the QM region. But as I consider one Na+ ion along with RNA atoms within the QM region it was showing that "Unable to correctly identify element SOD". Could you please help me or give me any advice about this error? Thanks in advance! Kaushik ------------------------------ Message: 36 Date: Thu, 11 Feb 2016 10:20:48 -0700 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] Quasi-harmonic Calculations To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOYxSOS0L8n-FXG_gGPOzs9h-=jAS5fNNxx+Mqxkyjz1Mg.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi, Just to add to what Jason said, just to even properly populate your mass-weighted covariance matrix you will need at least as many frames as you have rows (i.e. N = # atoms in your covariance matrix times 3). For a good estimate of the entropy I suspect you'll probably want at least 10 times that, although I'm sure some of the articles Jason pointed out have better recommendations. One measure you can use is to perform your quasi-harmonic calculation, then extend your simulations by N frames and observe how your calculated values change. -Dan On Thu, Feb 11, 2016 at 9:42 AM, Jason Swails <jason.swails.gmail.com> wrote: > On Thu, Feb 11, 2016 at 10:34 AM, Aronica, Pietro < > pietro.aronica07.imperial.ac.uk> wrote: > >> Hello, >> I wanted to perform quasi-harmonic calculations of an interaction I have >> to estimate the entropy. I have been told that in order for this to work >> properly, the simulation needs to be of at least a certain length. I've >> also been told that this issue had been discussed on the mailing list >> before, but I have failed to find relevant information, just hints, and the >> tutorials are rather vague on the subject. Where can I find exact >> information on how quasi-harmonic calculations ought to be run? >> > > Journal articles. There seem to be some promising hits on Google Scholar: > https://scholar.google.com/scholar?hl=en&q=quasi-harmonic+entropy&btnG=&as_sdt=1%2C5&as_sdtp= > > It may also take some amount of "try it and see" (e.g., in terms of how > many frames to include, etc.). > > HTH, > Jason > > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > _______________________________________________ > 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) ------------------------------ Message: 37 Date: Thu, 11 Feb 2016 11:27:08 -0600 From: Carlos Romero <carlos.rom.74he.gmail.com> Subject: [AMBER] interpret results To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAA_maK2+kQuKzrRwkj=iG4nBrge1AwzuFkHf-pvnUZGg+sEY8Q.mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi dear all. I am working in protein interactions en presence of ions. I make simulations according to AMBER tutorials. The procedure I follow is the next: When I have a complex, I separate receptor and ligand with a text editor. I add ions, solvate, do minimizations, heating and Dynamic simulations according to Tutorials. When the dynamics finish, normally I get a PDB file by ampbdb utility from both molecules, receptor and ligands, and I make a docking using Hex 6.3. It is the way I thought I could observe a conformational change in both molecules and see if in presence of ions have the same behavior. But I was looking in literature if this procedure was correct and I found that the way of analyse the results is diferent. My question is: could anybody help me in suggets literature for what means a dinamyc molecular simulation?, and how can I interpret results? I searched in the internet but it is a lot of information and I really don't understand so much. I appreciate your comments. Regards ------------------------------ Message: 38 Date: Thu, 11 Feb 2016 20:56:50 +0100 From: Batuhan Kav <bkav13.ku.edu.tr> Subject: [AMBER] Error: Bad > topology file. To: amber.ambermd.org Message-ID: <D1FB6DE5-0074-486D-8FB8-32A5D336FEAC.ku.edu.tr> Content-Type: text/plain; charset=utf-8 Dear All, I am simulating a system of two sugar molecules in water box. I obtain the structure from glycam website, and bind monosaccharides using bond command in tleap. When running equilibration run, a faced with the error ?Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM?. Interestingly (for me, at least), both minimization and heating runs did not give any errors, although I am using sander.MPI for all pre-production runs. I know this is a known bug in tleap, and also know how to fix it. I wanted to ask if it would be safe to think that bond command worked correctly when I do not get any ?bad topology? errors. With the same bond commands in tleap I have created many systems, and this is the first time that I got such an error. I use AmberTools15, if it helps. Best, Batuhan ------------------------------ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber End of AMBER Digest, Vol 1483, Issue 1 ************************************** _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Feb 11 2016 - 21:30:04 PST