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-- *Regards* Garima Singh AcSIR-PhD Fellow Biotechnology Division Central Institute Of Medicinal And Aromatic Plant CSIR-CIMAP Lucknow garimabioinfo.gmail.com *INDIA* Please don't print this e-mail unless you really need to. Be Green ! On Thu, Jun 7, 2018 at 12:30 AM, <amber-request.ambermd.org> wrote: > Send AMBER mailing list submissions to > amber.ambermd.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.ambermd.org/mailman/listinfo/amber > or, via email, send a message with subject or body 'help' to > amber-request.ambermd.org > > You can reach the person managing the list at > amber-owner.ambermd.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of AMBER digest..." > > > AMBER Mailing List Digest > > Today's Topics: > > 1. Re: how to calculate the mass center distance between > adjacent repeat units of one polymer chain (Daniel Roe) > 2. Re: how to calculate the mass center distance between > adjacent repeat units of one polymer chain (???) > 3. protein sampling efficacy (Lei Zhao) > 4. Re: Using Pytraj to read and write velocity files (Korey M Reid) > 5. Re: Using Pytraj to read and write velocity files (Hai Nguyen) > 6. NaN in NEB output (Aravind Ravichandran) > 7. Queries regarding bond command in leap (Aravind Ravichandran) > 8. Re: Queries regarding bond command in leap (Bill Ross) > 9. Re: Queries regarding bond command in leap (Aravind Ravichandran) > 10. Re: Conda Installation error > (andreas.tosstorff.cup.uni-muenchen.de) > 11. Re: Using Pytraj to read and write velocity files (Korey M Reid) > 12. Amber18 and CUDA 9.2 (Nikolay N. Kuzmich) > 13. Advanced restraints in protein mutation (Simon Kit Sang Chu) > 14. Amber DSSP : Secondary structure (Garima Singh) > 15. Re: Conda Installation error (David A Case) > 16. Re: Amber18 and CUDA 9.2 (David A Case) > 17. Re: NaN in NEB output (Carlos Simmerling) > 18. Re: compatibility of graphic card and Amber (Ross Walker) > 19. Re: Amber DSSP : Secondary structure (Daniel Roe) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 5 Jun 2018 15:11:53 -0400 > From: Daniel Roe <daniel.r.roe.gmail.com> > Subject: Re: [AMBER] how to calculate the mass center distance between > adjacent repeat units of one polymer chain > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAAC0qObxe-sb_dyPZioMV61e8PFQg_39Ufn6=6Rjh7q > U4wv7cg.mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > You can use the new loop and script variable functionality in cpptraj > (you need an up-to-date version, either from GitHub or Amber18). > > For example: > > for i=1;i<10;i++ > for j=2;j<10;j++ > distance d_$i_$j out dist.dat > done > done > > Or something like: > > for atoms A0 inmask :1-10 i=1;i++ > distance d$i :11 $A0 out dist.dat > done > > See the manual for more details, in particular look at the new 'for' > and 'set' commands (section 29.3 Variables and Control Structures). > > You can also use pytraj as Wesley suggested. > > -Dan > > On Tue, Jun 5, 2018 at 12:53 PM, ??? <tangyuanhui08.126.com> wrote: > > Hello all, > > > > > > This is Yuanhui. I want to calculate the distance between two residues > as :i and :j, and i, j can be changed during a loop. However, the distance > mask doesn't recognize the word :i. The input file is written like this: > > > > > > parm *.prmtop > > trajin md15.mdcrd 1 last 200 > > i=2 > > j=3 > > distance dist :i :j out dist.dat > > > > > > Is there a way can make the cpptraj recognize the variable 'i' and 'j', > because I want to change their values. > > Best wishes! > > > > > > > > -- > > > > Dr. Yuanhui Tang > > Ralph E. Martin Department of Chemical Engineering > > University of Arkansas > > Cato Springs Research Center > > Fayetteville, AR 72701 > > email: yt006.uark.edu > > voice: (479) 409-9989 > > > > > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > ------------------------------ > > Message: 2 > Date: Wed, 6 Jun 2018 04:09:17 +0800 (CST) > From: ??? <tangyuanhui08.126.com> > Subject: Re: [AMBER] how to calculate the mass center distance between > adjacent repeat units of one polymer chain > To: "AMBER Mailing List" <amber.ambermd.org> > Message-ID: <efe4fd3.23f.163d191665d.Coremail.tangyuanhui08.126.com> > Content-Type: text/plain; charset=GBK > > > Thank you. I have learned that. Thank you for your suggestions. > > > > > -- > > > Yuanhui Tang > > Doctor Candidate > > Beijing Key Laboratory for Membrane Materials and Engineering > > Department of Chemical Engineering, Tsinghua University > > Beijing 100084, PR China > > Tel: 86-10-62794742; > > Email: tangyh08.gmail.com > > > > > At 2018-06-06 01:13:23, "Wesley Michael Botello-Smith" <wmsmith.uci.edu> > wrote: > >I would use pytraj to this. You can accomplish the same thing using the " > >pytraj.analysis.vector.center" command > >see: http://amber-md.github.io/pytraj/latest/_api/pytraj.vector.html > >That way you have access to python syntax and you can run your loop in > >python. > > > >You could even then use pytraj.compute or pytraj.pmap if you want to do > the > >loop for you. These commands can take a python style list of individual > >commands as input and will automatically run each one. The pmap command > >will even let you run them in parallel. > > > >If you really want to do this in cpptraj, you would have to write each i j > >combination explicitly. Before I learned pytraj, I would usually write a > >bash script to generate the cpptraj input script to do that sort of > >iteration. > > > >Hope that helps! > > > >On Tue, Jun 5, 2018 at 9:53 AM, ??? <tangyuanhui08.126.com> wrote: > > > >> Hello all, > >> > >> > >> This is Yuanhui. I want to calculate the distance between two residues > as > >> :i and :j, and i, j can be changed during a loop. However, the distance > >> mask doesn't recognize the word :i. The input file is written like this: > >> > >> > >> parm *.prmtop > >> trajin md15.mdcrd 1 last 200 > >> i=2 > >> j=3 > >> distance dist :i :j out dist.dat > >> > >> > >> Is there a way can make the cpptraj recognize the variable 'i' and 'j', > >> because I want to change their values. > >> Best wishes! > >> > >> > >> > >> -- > >> > >> Dr. Yuanhui Tang > >> Ralph E. Martin Department of Chemical Engineering > >> University of Arkansas > >> Cato Springs Research Center > >> Fayetteville, AR 72701 > >> email: yt006.uark.edu > >> voice: (479) 409-9989 > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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: 3 > Date: Wed, 6 Jun 2018 11:10:31 +0800 > From: Lei Zhao <jackyzhao010.gmail.com> > Subject: [AMBER] protein sampling efficacy > To: amber <amber.ambermd.org> > Message-ID: <A477A2B7-6818-45AB-B648-5443292FC610.gmail.com> > Content-Type: text/plain; charset=utf-8 > > Hi everyone, > Several research articles have showed that MC method exhibited more > powerful to protein sampling than MD method. I am wondering that MC could > be more suitable for protein design? > Recently, I have performed long term MD method for protein design > (3?s). However, I have repeated long-term MD simulation to evaluate binding > affinity improvement through MM-GBSA. I found that reproducibility of MD > could be a issue. > Maybe this could be protein sampling problem? > Could anyone give some suggestions? > > Thanks > > Lei > > > ------------------------------ > > Message: 4 > Date: Wed, 6 Jun 2018 04:03:40 +0000 > From: Korey M Reid <koreyr.unr.edu> > Subject: Re: [AMBER] Using Pytraj to read and write velocity files > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CY1PR0101MB0585717EE6B355EF3E9A0C6FD1650.CY1PR0101MB0585. > prod.exchangelabs.com> > > Content-Type: text/plain; charset="us-ascii" > > Hello Hai, > > I have produced separate coordinate and velocity netcdf trajectory files > with input options ntwx=5 and ntwv=2.5. This is so I can accurately > calculate the midpoint of the velocity trajectory timepoints so that they > match the coordinate timepoints. I would like to perform this with pytraj. > However when I attempt to load the velocity trajectory files like so: > > >traj_vel = pt.load('vel.netcdf',top='top.parm7') > > the velocities fail to load. When I check the trajectory: > > >traj_vel > > the output reads: > > pytraj.Trajectory, 0 frames: > Size: 0.000000 (GB) > <Topology: 30220 atoms, 8815 residues, 8525 mols, PBC with box type = > truncoct> > > > and if I attempt to follow your example (thank you for this example I used > it as a reference some time ago to extract the t0-dt/2 frame some time ago) > running the following command in python: > > >traj_vel.velocities > > there is no output, which supports the 0GB trajectory file which from my > simulations should read 4GB or so. This is why I am curious if like cpptraj > there is an option to read velocities as coordinates since I am having such > difficulty finding a solution to my needs. > > > Thank you for your help! > > > With best, > > Korey > > > ________________________________ > From: Hai Nguyen <nhai.qn.gmail.com> > Sent: Saturday, June 2, 2018 3:44:59 PM > To: AMBER Mailing List > Subject: Re: [AMBER] Using Pytraj to read and write velocity files > > Hi Korey, > > Can you elaborate about "unsuccessful at reading in velocity netcdf files > produced from simulation"? (e.g: what's command you used?) > PS: I've posted an example a while ago and I hope that helps: > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Farchive.ambermd.org%2F201805%2F0078.html&data= > 01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da82de% > 7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=%2FxFdna% > 2Bz5vU1n1eF5sI0jnssVAVJFKIIXpzms1bIZfg%3D&reserved=0 > > Hai > > > On Sat, Jun 2, 2018 at 12:08 AM, Korey M Reid <koreyr.unr.edu> wrote: > > > Dear all, > > > > I have been able to extract velocity coordinates from a restart file up > to > > know for calculations down the line. However, I have been unsuccessful at > > reading in velocity netcdf files produced from simulation. Is there a > flag > > that I have been unable to identify such as in cpptraj's usevelascoords? > > The reason I ask is that I would like to code my analysis in python and I > > need to slice things in an unexpected way and would like to avoid > rerunning > > some long simulations. As always thank you for your input and time! > > > > > > With best, > > > > Korey Reid > > > > University of Nevada, Reno > > > > Chemistry Dept. > > > > Emphasis: Energy flow, Barrier conductance accross proteins, entropy > meters > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo% > 2Famber&data=01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da > 82de%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=1% > 2BHtFB0MaHN7eTwd4PvS97mzTJZXex9ilKNgWvc2Igs%3D&reserved=0 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo% > 2Famber&data=01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da > 82de%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=1% > 2BHtFB0MaHN7eTwd4PvS97mzTJZXex9ilKNgWvc2Igs%3D&reserved=0 > > > ------------------------------ > > Message: 5 > Date: Wed, 6 Jun 2018 00:21:08 -0400 > From: Hai Nguyen <nhai.qn.gmail.com> > Subject: Re: [AMBER] Using Pytraj to read and write velocity files > To: AMBER Mailing List <amber.ambermd.org> > Cc: Daniel Roe <daniel.r.roe.gmail.com> > Message-ID: > <CAFNMPM-MK2w0ZGex5LSCG0dUCp-CqyrFo8Ukqp5oaP6AY_6ApQ.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > uhm, clearly pytraj does not know how to read your velocity trajectory. I > will let Dan Roe to comment about the cpptraj's option. > > Meanwhile, you can try to use parmed to read your netcdf file (hope that > works) and pass > > In [17]: import parmed as pmd > > > In [18]: f = parmed.utils.netcdf.netcdf_file('files/tz2.nc') > > > In [19]: f.variables > > Out[19]: > > {'cell_angular': <parmed.utils.netcdf.netcdf_variable at 0x1131ea668>, > > 'cell_spatial': <parmed.utils.netcdf.netcdf_variable at 0x1131ea710>, > > 'coordinates': <parmed.utils.netcdf.netcdf_variable at 0x1131ea748>, > > 'spatial': <parmed.utils.netcdf.netcdf_variable at 0x1131ea588>, > > 'time': <parmed.utils.netcdf.netcdf_variable at 0x1131ea6a0>} > > > In [20]: f.variables['coordinates'].data # check f.variables to find your > keywords and replace "coordinates" > > > # Then reconstruct a pytraj's Trajectory > > In [21]: import pytraj as pt > > In [22]: traj = pt.Trajectory(xyz=f.variables['coordinates'].data, > top=your.top) > > # Then do anything you want wit this. > > > # Above example shows way to get the data (e.g: coordinates, velocity) and > then you can update the traj > > traj.xyz = your_xyz > > traj.velocity = your_velocity > > Hai > > On Wed, Jun 6, 2018 at 12:03 AM, Korey M Reid <koreyr.unr.edu> wrote: > > > Hello Hai, > > > > I have produced separate coordinate and velocity netcdf trajectory files > > with input options ntwx=5 and ntwv=2.5. This is so I can accurately > > calculate the midpoint of the velocity trajectory timepoints so that they > > match the coordinate timepoints. I would like to perform this with > pytraj. > > However when I attempt to load the velocity trajectory files like so: > > > > >traj_vel = pt.load('vel.netcdf',top='top.parm7') > > > > the velocities fail to load. When I check the trajectory: > > > > >traj_vel > > > > the output reads: > > > > pytraj.Trajectory, 0 frames: > > Size: 0.000000 (GB) > > <Topology: 30220 atoms, 8815 residues, 8525 mols, PBC with box type = > > truncoct> > > > > > > and if I attempt to follow your example (thank you for this example I > used > > it as a reference some time ago to extract the t0-dt/2 frame some time > ago) > > running the following command in python: > > > > >traj_vel.velocities > > > > there is no output, which supports the 0GB trajectory file which from my > > simulations should read 4GB or so. This is why I am curious if like > cpptraj > > there is an option to read velocities as coordinates since I am having > such > > difficulty finding a solution to my needs. > > > > > > Thank you for your help! > > > > > > With best, > > > > Korey > > > > > > ________________________________ > > From: Hai Nguyen <nhai.qn.gmail.com> > > Sent: Saturday, June 2, 2018 3:44:59 PM > > To: AMBER Mailing List > > Subject: Re: [AMBER] Using Pytraj to read and write velocity files > > > > Hi Korey, > > > > Can you elaborate about "unsuccessful at reading in velocity netcdf files > > produced from simulation"? (e.g: what's command you used?) > > PS: I've posted an example a while ago and I hope that helps: > > https://na01.safelinks.protection.outlook.com/?url= > > http%3A%2F%2Farchive.ambermd.org%2F201805%2F0078.html&data= > > 01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da82de% > > 7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=%2FxFdna% > > 2Bz5vU1n1eF5sI0jnssVAVJFKIIXpzms1bIZfg%3D&reserved=0 > > > > Hai > > > > > > On Sat, Jun 2, 2018 at 12:08 AM, Korey M Reid <koreyr.unr.edu> wrote: > > > > > Dear all, > > > > > > I have been able to extract velocity coordinates from a restart file up > > to > > > know for calculations down the line. However, I have been unsuccessful > at > > > reading in velocity netcdf files produced from simulation. Is there a > > flag > > > that I have been unable to identify such as in cpptraj's > usevelascoords? > > > The reason I ask is that I would like to code my analysis in python > and I > > > need to slice things in an unexpected way and would like to avoid > > rerunning > > > some long simulations. As always thank you for your input and time! > > > > > > > > > With best, > > > > > > Korey Reid > > > > > > University of Nevada, Reno > > > > > > Chemistry Dept. > > > > > > Emphasis: Energy flow, Barrier conductance accross proteins, entropy > > meters > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > https://na01.safelinks.protection.outlook.com/?url= > > http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo% > > 2Famber&data=01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da > > 82de%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=1% > > 2BHtFB0MaHN7eTwd4PvS97mzTJZXex9ilKNgWvc2Igs%3D&reserved=0 > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > https://na01.safelinks.protection.outlook.com/?url= > > http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo% > > 2Famber&data=01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da > > 82de%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=1% > > 2BHtFB0MaHN7eTwd4PvS97mzTJZXex9ilKNgWvc2Igs%3D&reserved=0 > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 6 > Date: Wed, 6 Jun 2018 10:11:51 +0530 (IST) > From: "Aravind Ravichandran" <raravind.ibab.ac.in> > Subject: [AMBER] NaN in NEB output > To: amber.ambermd.org > Message-ID: > <34648.158.144.176.250.1528260111.squirrel.webmail.ibab.ac.in> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Amber Users, > I am performing NEB having open and close forms of the protein as the end > points. I had performed minimization on the structures and started > heating the file as described in the tutorial > (http://ambermd.org/tutorials/advanced/tutorial5_amber11/section4.htm). > > This was my input- > Alanine NEB initial MD with small K > &cntrl > imin = 0, irest = 0, > ntc=1, ntf=1, > ntpr=1000, ntwx=1000, > ntb = 0, cut = 999.0, rgbmax=999.0, > igb = 1, saltcon=0.2, > nstlim = 80000, nscm=0, > dt = 0.0005, ig=-1, > ntt = 3, gamma_ln=1000.0, > tempi=0.0, temp0=300.0, > tgtfitmask=":77-222.CA,N,C", > tgtrmsmask=":1-70.CA,N,C", > ineb = 1,skmin = 10,skmax = 10, > nmropt=1, > / > &wt type='TEMP0', istep1=0,istep2=70000, > value1=0.0, value2=300.0 > / > &wt type='END' > / > > I created 32 replicas, with the first 16 using copies of the > str1.inpcrd(open) and the second 16 using copies of the > str2.inpcrd(close). > > I had the following values in input file- > > NEB replicate breakdown: > Energy for replicate 1 = -7948.5700 > Energy for replicate 2 = -4794.8407 > Energy for replicate 3 = -4802.4589 > Energy for replicate 4 = -4782.0042 > Energy for replicate 5 = -4851.8885 > Energy for replicate 6 = -4648.3221 > Energy for replicate 7 = -4574.8053 > Energy for replicate 8 = -4340.0242 > Energy for replicate 9 = -3886.3826 > Energy for replicate 10 = -3598.1682 > Energy for replicate 11 = -3078.5674 > Energy for replicate 12 = -2894.6292 > Energy for replicate 13 = -2538.0334 > Energy for replicate 14 = -2289.5568 > Energy for replicate 15 = 439.5811 > Energy for replicate 16 = NaN > Energy for replicate 17 = NaN > Energy for replicate 18 = 53846.6821 > Energy for replicate 19 = 2683.6924 > Energy for replicate 20 = -1703.6992 > Energy for replicate 21 = -2834.8332 > Energy for replicate 22 = -3560.3560 > Energy for replicate 23 = -3806.8150 > Energy for replicate 24 = -4266.6744 > Energy for replicate 25 = -4554.9216 > Energy for replicate 26 = -4702.1741 > Energy for replicate 27 = -4909.6870 > Energy for replicate 28 = -4867.9026 > Energy for replicate 29 = -4854.1495 > Energy for replicate 30 = -4844.1450 > Energy for replicate 31 = -4926.5483 > Energy for replicate 32 = -7999.0321 > Total Energy of replicates = NaN > > > Whys is there a NaN in the output file. Is it okay to have it? > How to correct it ? > > > Thank you, > Aravind R > > > > > > ------------------------------ > > Message: 7 > Date: Wed, 6 Jun 2018 10:36:34 +0530 (IST) > From: "Aravind Ravichandran" <raravind.ibab.ac.in> > Subject: [AMBER] Queries regarding bond command in leap > To: amber.ambermd.org > Message-ID: > <34593.158.144.176.250.1528261594.squirrel.webmail.ibab.ac.in> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Amber Users, > I have two Zn coordination systems in my protein. I cleaned my PDB and > executed the following commands in leap. > > > tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB > addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } } > loadoff atomic_ions.lib > loadamberparams frcmod.ions1lsm_hfe_tip3p > loadamberprep ZAFF.prep > loadamberparams ZAFF.frcmod > mol = loadpdb wt_clean2.pdb > bond mol.1410.ZN mol.888.SG > bond mol.1410.ZN mol.895.SG > bond mol.1410.ZN mol.898.SG > bond mol.1410.ZN mol.814.SG > > > As I execute the bond command I get the following errors for each bond > command. > > bond: Argument #2 is type String must be of type: [atom] > usage: bond <atom1> <atom2> [order] > > Whereas when I use the same bond command for the other Zn, it doesn't > throw any error. > bond mol.1409.ZN mol.70.SG > bond mol.1409.ZN mol.72.SG > bond mol.1409.ZN mol.85.SG > bond mol.1409.ZN mol.88.SG > > There were no errors thrown for these second set of bond commands. > > Can someone help me why the leap is throwing the error, even though I have > used pointer pointing only atoms in the command? > > These are my Zn coordination residues- > ATOM 1147 N CY1 70 128.847 145.112 153.017 -0.4157 1.5500 > N > ATOM 1148 H CY1 70 128.432 144.515 152.323 0.2719 1.3000 > H > ATOM 1149 CA CY1 70 128.266 145.150 154.346 0.0213 1.7000 > C > ATOM 1150 HA CY1 70 128.217 146.179 154.676 0.1124 1.2000 > H > ATOM 1151 CB CY1 70 126.845 144.595 154.334 -0.1231 1.7000 > C > ATOM 1152 HB2 CY1 70 126.230 145.220 153.686 0.1112 1.2000 > H > ATOM 1153 HB3 CY1 70 126.867 143.586 153.920 0.1112 1.2000 > H > ATOM 1154 SG CY1 70 126.091 144.526 155.964 -0.3119 1.8000 > S > ATOM 1155 HG CY1 70 125.916 145.843 156.099 0.1933 1.2000 > H > ATOM 1156 C CY1 70 129.108 144.348 155.329 0.5973 1.7000 > C > ATOM 1157 O CY1 70 130.051 143.643 154.962 -0.5679 1.5000 > O > ATOM 1177 N CY1 72 127.753 142.043 157.573 -0.4157 1.5500 > N > ATOM 1178 H CY1 72 127.100 142.781 157.354 0.2719 1.3000 > H > ATOM 1179 CA CY1 72 127.278 140.670 157.691 0.0213 1.7000 > C > ATOM 1180 HA CY1 72 127.744 140.206 158.562 0.1124 1.2000 > H > ATOM 1181 CB CY1 72 125.770 140.648 157.906 -0.1231 1.7000 > C > ATOM 1182 HB2 CY1 72 125.478 139.618 158.113 0.1112 1.2000 > H > ATOM 1183 HB3 CY1 72 125.511 141.249 158.775 0.1112 1.2000 > H > ATOM 1184 SG CY1 72 124.841 141.209 156.480 -0.3119 1.8000 > S > ATOM 1185 HG CY1 72 125.072 142.514 156.657 0.1933 1.2000 > H > ATOM 1186 C CY1 72 127.645 139.855 156.460 0.5973 1.7000 > C > ATOM 1187 O CY1 72 128.032 138.688 156.573 -0.5679 1.5000 > O > ATOM 1408 N CY1 85 121.747 147.502 155.149 -0.4157 1.5500 > N > ATOM 1409 H CY1 85 122.695 147.802 155.321 0.2719 1.3000 > H > ATOM 1410 CA CY1 85 121.334 146.162 155.535 0.0213 1.7000 > C > ATOM 1411 HA CY1 85 120.732 145.733 154.731 0.1124 1.2000 > H > ATOM 1412 CB CY1 85 122.546 145.266 155.738 -0.1231 1.7000 > C > ATOM 1413 HB2 CY1 85 123.066 145.190 154.784 0.1112 1.2000 > H > ATOM 1414 HB3 CY1 85 123.236 145.725 156.436 0.1112 1.2000 > H > ATOM 1415 SG CY1 85 122.134 143.609 156.281 -0.3119 1.8000 > S > ATOM 1416 HG CY1 85 121.224 143.386 155.333 0.1933 1.2000 > H > ATOM 1417 C CY1 85 120.496 146.218 156.800 0.5973 1.7000 > C > ATOM 1418 O CY1 85 120.856 146.888 157.771 -0.5679 1.5000 > O > ATOM 1456 N CY1 88 122.152 144.186 160.031 -0.4157 1.5500 > N > ATOM 1457 H CY1 88 122.245 144.135 159.027 0.2719 1.3000 > H > ATOM 1458 CA CY1 88 123.047 145.084 160.746 0.0213 1.7000 > C > ATOM 1459 HA CY1 88 122.587 145.403 161.682 0.1124 1.2000 > H > ATOM 1460 CB CY1 88 124.373 144.431 161.069 -0.1231 1.7000 > C > ATOM 1461 HB2 CY1 88 124.990 145.154 161.604 0.1112 1.2000 > H > ATOM 1462 HB3 CY1 88 124.191 143.590 161.739 0.1112 1.2000 > H > ATOM 1463 SG CY1 88 125.318 143.834 159.645 -0.3119 1.8000 > S > ATOM 1464 HG CY1 88 125.259 144.970 158.949 0.1933 1.2000 > H > ATOM 1465 C CY1 88 123.259 146.307 159.873 0.5973 1.7000 > C > ATOM 1466 O CY1 88 123.516 146.172 158.676 -0.5679 1.5000 > O > ATOM 12993 N CY1 814 152.534 203.432 142.773 -0.4157 1.5500 > N > ATOM 12994 H CY1 814 153.509 203.476 143.029 0.2719 1.3000 > H > ATOM 12995 CA CY1 814 151.556 204.186 143.544 0.0213 1.7000 > C > ATOM 12996 HA CY1 814 150.550 203.820 143.332 0.1124 1.2000 > H > ATOM 12997 CB CY1 814 151.783 203.997 145.043 -0.1231 1.7000 > C > ATOM 12998 HB2 CY1 814 150.916 204.406 145.558 0.1112 1.2000 > H > ATOM 12999 HB3 CY1 814 151.822 202.930 145.259 0.1112 1.2000 > H > ATOM 13000 SG CY1 814 153.271 204.791 145.682 -0.3119 1.8000 > S > ATOM 13001 HG CY1 814 152.727 206.005 145.804 0.1933 1.2000 > H > ATOM 13002 C CY1 814 151.605 205.667 143.209 0.5973 1.7000 > C > ATOM 13003 O CY1 814 150.562 206.330 143.186 -0.5679 1.5000 > O > ATOM 14131 N CY1 888 155.373 203.452 151.566 -0.4157 1.5500 > N > ATOM 14132 H CY1 888 155.673 202.619 152.051 0.2719 1.3000 > H > ATOM 14133 CA CY1 888 154.598 203.319 150.345 0.0213 1.7000 > C > ATOM 14134 HA CY1 888 154.984 204.016 149.599 0.1124 1.2000 > H > ATOM 14135 CB CY1 888 154.714 201.910 149.774 -0.1231 1.7000 > C > ATOM 14136 HB2 CY1 888 155.764 201.695 149.574 0.1112 1.2000 > H > ATOM 14137 HB3 CY1 888 154.353 201.196 150.516 0.1112 1.2000 > H > ATOM 14138 SG CY1 888 153.778 201.677 148.251 -0.3119 1.8000 > S > ATOM 14139 HG CY1 888 154.477 202.538 147.509 0.1933 1.2000 > H > ATOM 14140 C CY1 888 153.133 203.649 150.597 0.5973 1.7000 > C > ATOM 14141 O CY1 888 152.695 203.855 151.730 -0.5679 1.5000 > O > ATOM 14223 N CY1 895 154.320 198.655 145.938 -0.4157 1.5500 > N > ATOM 14224 H CY1 895 154.150 199.456 146.529 0.2719 1.3000 > H > ATOM 14225 CA CY1 895 154.345 198.834 144.494 0.0213 1.7000 > C > ATOM 14226 HA CY1 895 153.750 198.039 144.045 0.1124 1.2000 > H > ATOM 14227 CB CY1 895 153.705 200.159 144.095 -0.1231 1.7000 > C > ATOM 14228 HB2 CY1 895 153.678 200.208 143.006 0.1112 1.2000 > H > ATOM 14229 HB3 CY1 895 152.672 200.168 144.434 0.1112 1.2000 > H > ATOM 14230 SG CY1 895 154.521 201.612 144.691 -0.3119 1.8000 > S > ATOM 14231 HG CY1 895 153.409 202.217 145.121 0.1933 1.2000 > H > ATOM 14232 C CY1 895 155.771 198.735 143.975 0.5973 1.7000 > C > ATOM 14233 O CY1 895 156.713 199.175 144.638 -0.5679 1.5000 > O > ATOM 14261 N CY1 898 158.440 201.434 143.766 -0.4157 1.5500 > N > ATOM 14262 H CY1 898 157.722 200.723 143.798 0.2719 1.3000 > H > ATOM 14263 CA CY1 898 158.934 201.971 145.027 0.0213 1.7000 > C > ATOM 14264 HA CY1 898 159.426 202.930 144.856 0.1124 1.2000 > H > ATOM 14265 CB CY1 898 157.763 202.222 145.971 -0.1231 1.7000 > C > ATOM 14266 HB2 CY1 898 157.014 202.794 145.444 0.1112 1.2000 > H > ATOM 14267 HB3 CY1 898 157.309 201.257 146.201 0.1112 1.2000 > H > ATOM 14268 SG CY1 898 158.124 203.024 147.533 -0.3119 1.8000 > S > ATOM 14269 HG CY1 898 159.108 202.200 147.893 0.1933 1.2000 > H > ATOM 14270 C CY1 898 159.938 201.034 145.679 0.5973 1.7000 > C > ATOM 14271 O CY1 898 160.746 201.465 146.506 -0.5679 1.5000 > O > HETATM22013 ZN ZN1 1408 124.407 143.482 157.414 1.00 0.00 > Zn > HETATM22014 ZN ZN1 1409 155.341 202.836 146.737 1.00 0.00 > Zn > > Thank you, > Aravind R > > > > > ------------------------------ > > Message: 8 > Date: Tue, 5 Jun 2018 22:21:44 -0700 > From: Bill Ross <ross.cgl.ucsf.edu> > Subject: Re: [AMBER] Queries regarding bond command in leap > To: amber.ambermd.org > Message-ID: <85d02f89-00ae-7940-ec59-5dfb0ee4839b.cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Note that the 'Argument #2' residues that succeed are in residue numbers > [70..88], however the ones that don't are in the 800's. The higher any > number goes, the more chance of the unexpected. In this case, if you > haven't tried, I suggest doing a savepdb, and checking that the residue > numbers are still numbered as you expect. > > Bill > > On 6/5/18 10:06 PM, Aravind Ravichandran wrote: > > Dear Amber Users, > > I have two Zn coordination systems in my protein. I cleaned my PDB and > > executed the following commands in leap. > > > > > > tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB > > addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } } > > loadoff atomic_ions.lib > > loadamberparams frcmod.ions1lsm_hfe_tip3p > > loadamberprep ZAFF.prep > > loadamberparams ZAFF.frcmod > > mol = loadpdb wt_clean2.pdb > > bond mol.1410.ZN mol.888.SG > > bond mol.1410.ZN mol.895.SG > > bond mol.1410.ZN mol.898.SG > > bond mol.1410.ZN mol.814.SG > > > > > > As I execute the bond command I get the following errors for each bond > > command. > > > > bond: Argument #2 is type String must be of type: [atom] > > usage: bond <atom1> <atom2> [order] > > > > Whereas when I use the same bond command for the other Zn, it doesn't > > throw any error. > > bond mol.1409.ZN mol.70.SG > > bond mol.1409.ZN mol.72.SG > > bond mol.1409.ZN mol.85.SG > > bond mol.1409.ZN mol.88.SG > > > > There were no errors thrown for these second set of bond commands. > > > > Can someone help me why the leap is throwing the error, even though I > have > > used pointer pointing only atoms in the command? > > > > These are my Zn coordination residues- > > ATOM 1147 N CY1 70 128.847 145.112 153.017 -0.4157 1.5500 > > N > > ATOM 1148 H CY1 70 128.432 144.515 152.323 0.2719 1.3000 > > H > > ATOM 1149 CA CY1 70 128.266 145.150 154.346 0.0213 1.7000 > > C > > ATOM 1150 HA CY1 70 128.217 146.179 154.676 0.1124 1.2000 > > H > > ATOM 1151 CB CY1 70 126.845 144.595 154.334 -0.1231 1.7000 > > C > > ATOM 1152 HB2 CY1 70 126.230 145.220 153.686 0.1112 1.2000 > > H > > ATOM 1153 HB3 CY1 70 126.867 143.586 153.920 0.1112 1.2000 > > H > > ATOM 1154 SG CY1 70 126.091 144.526 155.964 -0.3119 1.8000 > > S > > ATOM 1155 HG CY1 70 125.916 145.843 156.099 0.1933 1.2000 > > H > > ATOM 1156 C CY1 70 129.108 144.348 155.329 0.5973 1.7000 > > C > > ATOM 1157 O CY1 70 130.051 143.643 154.962 -0.5679 1.5000 > > O > > ATOM 1177 N CY1 72 127.753 142.043 157.573 -0.4157 1.5500 > > N > > ATOM 1178 H CY1 72 127.100 142.781 157.354 0.2719 1.3000 > > H > > ATOM 1179 CA CY1 72 127.278 140.670 157.691 0.0213 1.7000 > > C > > ATOM 1180 HA CY1 72 127.744 140.206 158.562 0.1124 1.2000 > > H > > ATOM 1181 CB CY1 72 125.770 140.648 157.906 -0.1231 1.7000 > > C > > ATOM 1182 HB2 CY1 72 125.478 139.618 158.113 0.1112 1.2000 > > H > > ATOM 1183 HB3 CY1 72 125.511 141.249 158.775 0.1112 1.2000 > > H > > ATOM 1184 SG CY1 72 124.841 141.209 156.480 -0.3119 1.8000 > > S > > ATOM 1185 HG CY1 72 125.072 142.514 156.657 0.1933 1.2000 > > H > > ATOM 1186 C CY1 72 127.645 139.855 156.460 0.5973 1.7000 > > C > > ATOM 1187 O CY1 72 128.032 138.688 156.573 -0.5679 1.5000 > > O > > ATOM 1408 N CY1 85 121.747 147.502 155.149 -0.4157 1.5500 > > N > > ATOM 1409 H CY1 85 122.695 147.802 155.321 0.2719 1.3000 > > H > > ATOM 1410 CA CY1 85 121.334 146.162 155.535 0.0213 1.7000 > > C > > ATOM 1411 HA CY1 85 120.732 145.733 154.731 0.1124 1.2000 > > H > > ATOM 1412 CB CY1 85 122.546 145.266 155.738 -0.1231 1.7000 > > C > > ATOM 1413 HB2 CY1 85 123.066 145.190 154.784 0.1112 1.2000 > > H > > ATOM 1414 HB3 CY1 85 123.236 145.725 156.436 0.1112 1.2000 > > H > > ATOM 1415 SG CY1 85 122.134 143.609 156.281 -0.3119 1.8000 > > S > > ATOM 1416 HG CY1 85 121.224 143.386 155.333 0.1933 1.2000 > > H > > ATOM 1417 C CY1 85 120.496 146.218 156.800 0.5973 1.7000 > > C > > ATOM 1418 O CY1 85 120.856 146.888 157.771 -0.5679 1.5000 > > O > > ATOM 1456 N CY1 88 122.152 144.186 160.031 -0.4157 1.5500 > > N > > ATOM 1457 H CY1 88 122.245 144.135 159.027 0.2719 1.3000 > > H > > ATOM 1458 CA CY1 88 123.047 145.084 160.746 0.0213 1.7000 > > C > > ATOM 1459 HA CY1 88 122.587 145.403 161.682 0.1124 1.2000 > > H > > ATOM 1460 CB CY1 88 124.373 144.431 161.069 -0.1231 1.7000 > > C > > ATOM 1461 HB2 CY1 88 124.990 145.154 161.604 0.1112 1.2000 > > H > > ATOM 1462 HB3 CY1 88 124.191 143.590 161.739 0.1112 1.2000 > > H > > ATOM 1463 SG CY1 88 125.318 143.834 159.645 -0.3119 1.8000 > > S > > ATOM 1464 HG CY1 88 125.259 144.970 158.949 0.1933 1.2000 > > H > > ATOM 1465 C CY1 88 123.259 146.307 159.873 0.5973 1.7000 > > C > > ATOM 1466 O CY1 88 123.516 146.172 158.676 -0.5679 1.5000 > > O > > ATOM 12993 N CY1 814 152.534 203.432 142.773 -0.4157 1.5500 > > N > > ATOM 12994 H CY1 814 153.509 203.476 143.029 0.2719 1.3000 > > H > > ATOM 12995 CA CY1 814 151.556 204.186 143.544 0.0213 1.7000 > > C > > ATOM 12996 HA CY1 814 150.550 203.820 143.332 0.1124 1.2000 > > H > > ATOM 12997 CB CY1 814 151.783 203.997 145.043 -0.1231 1.7000 > > C > > ATOM 12998 HB2 CY1 814 150.916 204.406 145.558 0.1112 1.2000 > > H > > ATOM 12999 HB3 CY1 814 151.822 202.930 145.259 0.1112 1.2000 > > H > > ATOM 13000 SG CY1 814 153.271 204.791 145.682 -0.3119 1.8000 > > S > > ATOM 13001 HG CY1 814 152.727 206.005 145.804 0.1933 1.2000 > > H > > ATOM 13002 C CY1 814 151.605 205.667 143.209 0.5973 1.7000 > > C > > ATOM 13003 O CY1 814 150.562 206.330 143.186 -0.5679 1.5000 > > O > > ATOM 14131 N CY1 888 155.373 203.452 151.566 -0.4157 1.5500 > > N > > ATOM 14132 H CY1 888 155.673 202.619 152.051 0.2719 1.3000 > > H > > ATOM 14133 CA CY1 888 154.598 203.319 150.345 0.0213 1.7000 > > C > > ATOM 14134 HA CY1 888 154.984 204.016 149.599 0.1124 1.2000 > > H > > ATOM 14135 CB CY1 888 154.714 201.910 149.774 -0.1231 1.7000 > > C > > ATOM 14136 HB2 CY1 888 155.764 201.695 149.574 0.1112 1.2000 > > H > > ATOM 14137 HB3 CY1 888 154.353 201.196 150.516 0.1112 1.2000 > > H > > ATOM 14138 SG CY1 888 153.778 201.677 148.251 -0.3119 1.8000 > > S > > ATOM 14139 HG CY1 888 154.477 202.538 147.509 0.1933 1.2000 > > H > > ATOM 14140 C CY1 888 153.133 203.649 150.597 0.5973 1.7000 > > C > > ATOM 14141 O CY1 888 152.695 203.855 151.730 -0.5679 1.5000 > > O > > ATOM 14223 N CY1 895 154.320 198.655 145.938 -0.4157 1.5500 > > N > > ATOM 14224 H CY1 895 154.150 199.456 146.529 0.2719 1.3000 > > H > > ATOM 14225 CA CY1 895 154.345 198.834 144.494 0.0213 1.7000 > > C > > ATOM 14226 HA CY1 895 153.750 198.039 144.045 0.1124 1.2000 > > H > > ATOM 14227 CB CY1 895 153.705 200.159 144.095 -0.1231 1.7000 > > C > > ATOM 14228 HB2 CY1 895 153.678 200.208 143.006 0.1112 1.2000 > > H > > ATOM 14229 HB3 CY1 895 152.672 200.168 144.434 0.1112 1.2000 > > H > > ATOM 14230 SG CY1 895 154.521 201.612 144.691 -0.3119 1.8000 > > S > > ATOM 14231 HG CY1 895 153.409 202.217 145.121 0.1933 1.2000 > > H > > ATOM 14232 C CY1 895 155.771 198.735 143.975 0.5973 1.7000 > > C > > ATOM 14233 O CY1 895 156.713 199.175 144.638 -0.5679 1.5000 > > O > > ATOM 14261 N CY1 898 158.440 201.434 143.766 -0.4157 1.5500 > > N > > ATOM 14262 H CY1 898 157.722 200.723 143.798 0.2719 1.3000 > > H > > ATOM 14263 CA CY1 898 158.934 201.971 145.027 0.0213 1.7000 > > C > > ATOM 14264 HA CY1 898 159.426 202.930 144.856 0.1124 1.2000 > > H > > ATOM 14265 CB CY1 898 157.763 202.222 145.971 -0.1231 1.7000 > > C > > ATOM 14266 HB2 CY1 898 157.014 202.794 145.444 0.1112 1.2000 > > H > > ATOM 14267 HB3 CY1 898 157.309 201.257 146.201 0.1112 1.2000 > > H > > ATOM 14268 SG CY1 898 158.124 203.024 147.533 -0.3119 1.8000 > > S > > ATOM 14269 HG CY1 898 159.108 202.200 147.893 0.1933 1.2000 > > H > > ATOM 14270 C CY1 898 159.938 201.034 145.679 0.5973 1.7000 > > C > > ATOM 14271 O CY1 898 160.746 201.465 146.506 -0.5679 1.5000 > > O > > HETATM22013 ZN ZN1 1408 124.407 143.482 157.414 1.00 0.00 > > Zn > > HETATM22014 ZN ZN1 1409 155.341 202.836 146.737 1.00 0.00 > > Zn > > > > Thank you, > > Aravind R > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > ------------------------------ > > Message: 9 > Date: Wed, 6 Jun 2018 11:13:43 +0530 (IST) > From: "Aravind Ravichandran" <raravind.ibab.ac.in> > Subject: Re: [AMBER] Queries regarding bond command in leap > To: "AMBER Mailing List" <amber.ambermd.org> > Message-ID: > <53927.158.144.176.250.1528263823.squirrel.webmail.ibab.ac.in> > Content-Type: text/plain;charset=iso-8859-1 > > Dear Bill, > Thank you for the suggestion. The numbering for residues were changed. > Since I had used pdb4amber to clean the pdb, the thought it would not be > numbering problem. It worked now. > > Thank you, > Aravind R > > Note that the 'Argument #2' residues that succeed are in residue numbers > > [70..88], however the ones that don't are in the 800's. The higher any > > number goes, the more chance of the unexpected. In this case, if you > > haven't tried, I suggest doing a savepdb, and checking that the residue > > numbers are still numbered as you expect. > > > > Bill > > > > On 6/5/18 10:06 PM, Aravind Ravichandran wrote: > >> Dear Amber Users, > >> I have two Zn coordination systems in my protein. I cleaned my PDB and > >> executed the following commands in leap. > >> > >> > >> tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB > >> addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } } > >> loadoff atomic_ions.lib > >> loadamberparams frcmod.ions1lsm_hfe_tip3p > >> loadamberprep ZAFF.prep > >> loadamberparams ZAFF.frcmod > >> mol = loadpdb wt_clean2.pdb > >> bond mol.1410.ZN mol.888.SG > >> bond mol.1410.ZN mol.895.SG > >> bond mol.1410.ZN mol.898.SG > >> bond mol.1410.ZN mol.814.SG > >> > >> > >> As I execute the bond command I get the following errors for each bond > >> command. > >> > >> bond: Argument #2 is type String must be of type: [atom] > >> usage: bond <atom1> <atom2> [order] > >> > >> Whereas when I use the same bond command for the other Zn, it doesn't > >> throw any error. > >> bond mol.1409.ZN mol.70.SG > >> bond mol.1409.ZN mol.72.SG > >> bond mol.1409.ZN mol.85.SG > >> bond mol.1409.ZN mol.88.SG > >> > >> There were no errors thrown for these second set of bond commands. > >> > >> Can someone help me why the leap is throwing the error, even though I > >> have > >> used pointer pointing only atoms in the command? > >> > >> These are my Zn coordination residues- > >> ATOM 1147 N CY1 70 128.847 145.112 153.017 -0.4157 1.5500 > >> N > >> ATOM 1148 H CY1 70 128.432 144.515 152.323 0.2719 1.3000 > >> H > >> ATOM 1149 CA CY1 70 128.266 145.150 154.346 0.0213 1.7000 > >> C > >> ATOM 1150 HA CY1 70 128.217 146.179 154.676 0.1124 1.2000 > >> H > >> ATOM 1151 CB CY1 70 126.845 144.595 154.334 -0.1231 1.7000 > >> C > >> ATOM 1152 HB2 CY1 70 126.230 145.220 153.686 0.1112 1.2000 > >> H > >> ATOM 1153 HB3 CY1 70 126.867 143.586 153.920 0.1112 1.2000 > >> H > >> ATOM 1154 SG CY1 70 126.091 144.526 155.964 -0.3119 1.8000 > >> S > >> ATOM 1155 HG CY1 70 125.916 145.843 156.099 0.1933 1.2000 > >> H > >> ATOM 1156 C CY1 70 129.108 144.348 155.329 0.5973 1.7000 > >> C > >> ATOM 1157 O CY1 70 130.051 143.643 154.962 -0.5679 1.5000 > >> O > >> ATOM 1177 N CY1 72 127.753 142.043 157.573 -0.4157 1.5500 > >> N > >> ATOM 1178 H CY1 72 127.100 142.781 157.354 0.2719 1.3000 > >> H > >> ATOM 1179 CA CY1 72 127.278 140.670 157.691 0.0213 1.7000 > >> C > >> ATOM 1180 HA CY1 72 127.744 140.206 158.562 0.1124 1.2000 > >> H > >> ATOM 1181 CB CY1 72 125.770 140.648 157.906 -0.1231 1.7000 > >> C > >> ATOM 1182 HB2 CY1 72 125.478 139.618 158.113 0.1112 1.2000 > >> H > >> ATOM 1183 HB3 CY1 72 125.511 141.249 158.775 0.1112 1.2000 > >> H > >> ATOM 1184 SG CY1 72 124.841 141.209 156.480 -0.3119 1.8000 > >> S > >> ATOM 1185 HG CY1 72 125.072 142.514 156.657 0.1933 1.2000 > >> H > >> ATOM 1186 C CY1 72 127.645 139.855 156.460 0.5973 1.7000 > >> C > >> ATOM 1187 O CY1 72 128.032 138.688 156.573 -0.5679 1.5000 > >> O > >> ATOM 1408 N CY1 85 121.747 147.502 155.149 -0.4157 1.5500 > >> N > >> ATOM 1409 H CY1 85 122.695 147.802 155.321 0.2719 1.3000 > >> H > >> ATOM 1410 CA CY1 85 121.334 146.162 155.535 0.0213 1.7000 > >> C > >> ATOM 1411 HA CY1 85 120.732 145.733 154.731 0.1124 1.2000 > >> H > >> ATOM 1412 CB CY1 85 122.546 145.266 155.738 -0.1231 1.7000 > >> C > >> ATOM 1413 HB2 CY1 85 123.066 145.190 154.784 0.1112 1.2000 > >> H > >> ATOM 1414 HB3 CY1 85 123.236 145.725 156.436 0.1112 1.2000 > >> H > >> ATOM 1415 SG CY1 85 122.134 143.609 156.281 -0.3119 1.8000 > >> S > >> ATOM 1416 HG CY1 85 121.224 143.386 155.333 0.1933 1.2000 > >> H > >> ATOM 1417 C CY1 85 120.496 146.218 156.800 0.5973 1.7000 > >> C > >> ATOM 1418 O CY1 85 120.856 146.888 157.771 -0.5679 1.5000 > >> O > >> ATOM 1456 N CY1 88 122.152 144.186 160.031 -0.4157 1.5500 > >> N > >> ATOM 1457 H CY1 88 122.245 144.135 159.027 0.2719 1.3000 > >> H > >> ATOM 1458 CA CY1 88 123.047 145.084 160.746 0.0213 1.7000 > >> C > >> ATOM 1459 HA CY1 88 122.587 145.403 161.682 0.1124 1.2000 > >> H > >> ATOM 1460 CB CY1 88 124.373 144.431 161.069 -0.1231 1.7000 > >> C > >> ATOM 1461 HB2 CY1 88 124.990 145.154 161.604 0.1112 1.2000 > >> H > >> ATOM 1462 HB3 CY1 88 124.191 143.590 161.739 0.1112 1.2000 > >> H > >> ATOM 1463 SG CY1 88 125.318 143.834 159.645 -0.3119 1.8000 > >> S > >> ATOM 1464 HG CY1 88 125.259 144.970 158.949 0.1933 1.2000 > >> H > >> ATOM 1465 C CY1 88 123.259 146.307 159.873 0.5973 1.7000 > >> C > >> ATOM 1466 O CY1 88 123.516 146.172 158.676 -0.5679 1.5000 > >> O > >> ATOM 12993 N CY1 814 152.534 203.432 142.773 -0.4157 1.5500 > >> N > >> ATOM 12994 H CY1 814 153.509 203.476 143.029 0.2719 1.3000 > >> H > >> ATOM 12995 CA CY1 814 151.556 204.186 143.544 0.0213 1.7000 > >> C > >> ATOM 12996 HA CY1 814 150.550 203.820 143.332 0.1124 1.2000 > >> H > >> ATOM 12997 CB CY1 814 151.783 203.997 145.043 -0.1231 1.7000 > >> C > >> ATOM 12998 HB2 CY1 814 150.916 204.406 145.558 0.1112 1.2000 > >> H > >> ATOM 12999 HB3 CY1 814 151.822 202.930 145.259 0.1112 1.2000 > >> H > >> ATOM 13000 SG CY1 814 153.271 204.791 145.682 -0.3119 1.8000 > >> S > >> ATOM 13001 HG CY1 814 152.727 206.005 145.804 0.1933 1.2000 > >> H > >> ATOM 13002 C CY1 814 151.605 205.667 143.209 0.5973 1.7000 > >> C > >> ATOM 13003 O CY1 814 150.562 206.330 143.186 -0.5679 1.5000 > >> O > >> ATOM 14131 N CY1 888 155.373 203.452 151.566 -0.4157 1.5500 > >> N > >> ATOM 14132 H CY1 888 155.673 202.619 152.051 0.2719 1.3000 > >> H > >> ATOM 14133 CA CY1 888 154.598 203.319 150.345 0.0213 1.7000 > >> C > >> ATOM 14134 HA CY1 888 154.984 204.016 149.599 0.1124 1.2000 > >> H > >> ATOM 14135 CB CY1 888 154.714 201.910 149.774 -0.1231 1.7000 > >> C > >> ATOM 14136 HB2 CY1 888 155.764 201.695 149.574 0.1112 1.2000 > >> H > >> ATOM 14137 HB3 CY1 888 154.353 201.196 150.516 0.1112 1.2000 > >> H > >> ATOM 14138 SG CY1 888 153.778 201.677 148.251 -0.3119 1.8000 > >> S > >> ATOM 14139 HG CY1 888 154.477 202.538 147.509 0.1933 1.2000 > >> H > >> ATOM 14140 C CY1 888 153.133 203.649 150.597 0.5973 1.7000 > >> C > >> ATOM 14141 O CY1 888 152.695 203.855 151.730 -0.5679 1.5000 > >> O > >> ATOM 14223 N CY1 895 154.320 198.655 145.938 -0.4157 1.5500 > >> N > >> ATOM 14224 H CY1 895 154.150 199.456 146.529 0.2719 1.3000 > >> H > >> ATOM 14225 CA CY1 895 154.345 198.834 144.494 0.0213 1.7000 > >> C > >> ATOM 14226 HA CY1 895 153.750 198.039 144.045 0.1124 1.2000 > >> H > >> ATOM 14227 CB CY1 895 153.705 200.159 144.095 -0.1231 1.7000 > >> C > >> ATOM 14228 HB2 CY1 895 153.678 200.208 143.006 0.1112 1.2000 > >> H > >> ATOM 14229 HB3 CY1 895 152.672 200.168 144.434 0.1112 1.2000 > >> H > >> ATOM 14230 SG CY1 895 154.521 201.612 144.691 -0.3119 1.8000 > >> S > >> ATOM 14231 HG CY1 895 153.409 202.217 145.121 0.1933 1.2000 > >> H > >> ATOM 14232 C CY1 895 155.771 198.735 143.975 0.5973 1.7000 > >> C > >> ATOM 14233 O CY1 895 156.713 199.175 144.638 -0.5679 1.5000 > >> O > >> ATOM 14261 N CY1 898 158.440 201.434 143.766 -0.4157 1.5500 > >> N > >> ATOM 14262 H CY1 898 157.722 200.723 143.798 0.2719 1.3000 > >> H > >> ATOM 14263 CA CY1 898 158.934 201.971 145.027 0.0213 1.7000 > >> C > >> ATOM 14264 HA CY1 898 159.426 202.930 144.856 0.1124 1.2000 > >> H > >> ATOM 14265 CB CY1 898 157.763 202.222 145.971 -0.1231 1.7000 > >> C > >> ATOM 14266 HB2 CY1 898 157.014 202.794 145.444 0.1112 1.2000 > >> H > >> ATOM 14267 HB3 CY1 898 157.309 201.257 146.201 0.1112 1.2000 > >> H > >> ATOM 14268 SG CY1 898 158.124 203.024 147.533 -0.3119 1.8000 > >> S > >> ATOM 14269 HG CY1 898 159.108 202.200 147.893 0.1933 1.2000 > >> H > >> ATOM 14270 C CY1 898 159.938 201.034 145.679 0.5973 1.7000 > >> C > >> ATOM 14271 O CY1 898 160.746 201.465 146.506 -0.5679 1.5000 > >> O > >> HETATM22013 ZN ZN1 1408 124.407 143.482 157.414 1.00 0.00 > >> Zn > >> HETATM22014 ZN ZN1 1409 155.341 202.836 146.737 1.00 0.00 > >> Zn > >> > >> Thank you, > >> Aravind R > >> > >> > >> _______________________________________________ > >> 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: 10 > Date: Wed, 6 Jun 2018 08:41:44 +0100 > From: <andreas.tosstorff.cup.uni-muenchen.de> > Subject: Re: [AMBER] Conda Installation error > To: "'AMBER Mailing List'" <amber.ambermd.org>, "'Scott Brozell'" > <sbrozell.rci.rutgers.edu> > Message-ID: <000001d3fd69$d4c85ad0$7e591070$.cup.uni-muenchen.de> > Content-Type: text/plain; charset="us-ascii" > > Hi all, > > I am using anaconda on Windows 10. It's still not working, also with the > command you suggested. > > > Here's the output: > > >conda install ambertools -c http://ambermd.org/downloads/ > ambertools/conda/ > Solving environment: failed > > PackagesNotFoundError: The following packages are not available from > current > channels: > > - ambertools > > Current channels: > > - http://ambermd.org/downloads/ambertools/conda/win-64 > - http://ambermd.org/downloads/ambertools/conda/noarch > - https://conda.anaconda.org/salilab/win-64 > - https://conda.anaconda.org/salilab/noarch > - https://repo.anaconda.com/pkgs/main/win-64 > - https://repo.anaconda.com/pkgs/main/noarch > - https://repo.anaconda.com/pkgs/free/win-64 > - https://repo.anaconda.com/pkgs/free/noarch > - https://repo.anaconda.com/pkgs/r/win-64 > - https://repo.anaconda.com/pkgs/r/noarch > - https://repo.anaconda.com/pkgs/pro/win-64 > - https://repo.anaconda.com/pkgs/pro/noarch > - https://repo.anaconda.com/pkgs/msys2/win-64 > - https://repo.anaconda.com/pkgs/msys2/noarch > > > -----Original Message----- > From: Hai Nguyen <nhai.qn.gmail.com> > Sent: Thursday, May 31, 2018 5:12 PM > To: AMBER Mailing List <amber.ambermd.org>; Scott Brozell > <sbrozell.rci.rutgers.edu> > Subject: Re: [AMBER] Conda Installation error > > On Thu, May 31, 2018 at 12:06 PM, Scott Brozell <sbrozell.rci.rutgers.edu> > wrote: > > > Hi, > > > > Possibly just a typo; this seems to be working for me: > > > > conda install ambertools -c > > http://ambermd.org/downloads/ambertools/conda/ > > > > > .Scott: Hi, with which ambertools version and platform (your os)? > > .Andreas: Which platform are you using? > > Hai > > scott > > > > On Thu, May 31, 2018 at 10:18:30AM -0400, Hai Nguyen wrote: > > > > > > Yes, it's still available. We will try to resolve this issue asap. > > > Thanks > > > > > > On Wed, May 30, 2018 at 1:51 PM, > > > <andreas.tosstorff.cup.uni-muenchen.de> > > > > I am trying to install ambertools through conda, but it does not > > > > seem > > to be > > > > available: > > > > Here's the command and the output: > > > > conda install ambertools=18 -c > > > > http://ambermd.org/downloads/ambertools/conda/ > > > > Solving environment: failed > > > > > > > > PackagesNotFoundError: The following packages are not available > > > > from current > > > > channels: > > > > - ambertools=18 > > > > Is the Conda installation option still available? > > > > _______________________________________________ > > 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: Wed, 6 Jun 2018 07:50:32 +0000 > From: Korey M Reid <koreyr.unr.edu> > Subject: Re: [AMBER] Using Pytraj to read and write velocity files > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CY1PR0101MB0585C4B9B07AFF9F067EF7A2D1650.CY1PR0101MB0585. > prod.exchangelabs.com> > > Content-Type: text/plain; charset="us-ascii" > > thank you so very much this is exactly what I was looking for! It is an > excellent solution! > > Have an awesome week! > > > With gratitude, > > Korey > > ________________________________ > From: Hai Nguyen <nhai.qn.gmail.com> > Sent: Tuesday, June 5, 2018 9:21:08 PM > To: AMBER Mailing List > Cc: Daniel Roe > Subject: Re: [AMBER] Using Pytraj to read and write velocity files > > uhm, clearly pytraj does not know how to read your velocity trajectory. I > will let Dan Roe to comment about the cpptraj's option. > > Meanwhile, you can try to use parmed to read your netcdf file (hope that > works) and pass > > In [17]: import parmed as pmd > > > In [18]: f = parmed.utils.netcdf.netcdf_file('files/tz2.nc') > > > In [19]: f.variables > > Out[19]: > > {'cell_angular': <parmed.utils.netcdf.netcdf_variable at 0x1131ea668>, > > 'cell_spatial': <parmed.utils.netcdf.netcdf_variable at 0x1131ea710>, > > 'coordinates': <parmed.utils.netcdf.netcdf_variable at 0x1131ea748>, > > 'spatial': <parmed.utils.netcdf.netcdf_variable at 0x1131ea588>, > > 'time': <parmed.utils.netcdf.netcdf_variable at 0x1131ea6a0>} > > > In [20]: f.variables['coordinates'].data # check f.variables to find your > keywords and replace "coordinates" > > > # Then reconstruct a pytraj's Trajectory > > In [21]: import pytraj as pt > > In [22]: traj = pt.Trajectory(xyz=f.variables['coordinates'].data, > top=your.top) > > # Then do anything you want wit this. > > > # Above example shows way to get the data (e.g: coordinates, velocity) and > then you can update the traj > > traj.xyz = your_xyz > > traj.velocity = your_velocity > > Hai > > On Wed, Jun 6, 2018 at 12:03 AM, Korey M Reid <koreyr.unr.edu> wrote: > > > Hello Hai, > > > > I have produced separate coordinate and velocity netcdf trajectory files > > with input options ntwx=5 and ntwv=2.5. This is so I can accurately > > calculate the midpoint of the velocity trajectory timepoints so that they > > match the coordinate timepoints. I would like to perform this with > pytraj. > > However when I attempt to load the velocity trajectory files like so: > > > > >traj_vel = pt.load('vel.netcdf',top='top.parm7') > > > > the velocities fail to load. When I check the trajectory: > > > > >traj_vel > > > > the output reads: > > > > pytraj.Trajectory, 0 frames: > > Size: 0.000000 (GB) > > <Topology: 30220 atoms, 8815 residues, 8525 mols, PBC with box type = > > truncoct> > > > > > > and if I attempt to follow your example (thank you for this example I > used > > it as a reference some time ago to extract the t0-dt/2 frame some time > ago) > > running the following command in python: > > > > >traj_vel.velocities > > > > there is no output, which supports the 0GB trajectory file which from my > > simulations should read 4GB or so. This is why I am curious if like > cpptraj > > there is an option to read velocities as coordinates since I am having > such > > difficulty finding a solution to my needs. > > > > > > Thank you for your help! > > > > > > With best, > > > > Korey > > > > > > ________________________________ > > From: Hai Nguyen <nhai.qn.gmail.com> > > Sent: Saturday, June 2, 2018 3:44:59 PM > > To: AMBER Mailing List > > Subject: Re: [AMBER] Using Pytraj to read and write velocity files > > > > Hi Korey, > > > > Can you elaborate about "unsuccessful at reading in velocity netcdf files > > produced from simulation"? (e.g: what's command you used?) > > PS: I've posted an example a while ago and I hope that helps: > > https://na01.safelinks.protection.outlook.com/?url= > > http%3A%2F%2Farchive.ambermd.org%2F201805%2F0078.html&data= > > 01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da82de% > > 7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=%2FxFdna% > > 2Bz5vU1n1eF5sI0jnssVAVJFKIIXpzms1bIZfg%3D&reserved=0 > > > > Hai > > > > > > On Sat, Jun 2, 2018 at 12:08 AM, Korey M Reid <koreyr.unr.edu> wrote: > > > > > Dear all, > > > > > > I have been able to extract velocity coordinates from a restart file up > > to > > > know for calculations down the line. However, I have been unsuccessful > at > > > reading in velocity netcdf files produced from simulation. Is there a > > flag > > > that I have been unable to identify such as in cpptraj's > usevelascoords? > > > The reason I ask is that I would like to code my analysis in python > and I > > > need to slice things in an unexpected way and would like to avoid > > rerunning > > > some long simulations. As always thank you for your input and time! > > > > > > > > > With best, > > > > > > Korey Reid > > > > > > University of Nevada, Reno > > > > > > Chemistry Dept. > > > > > > Emphasis: Energy flow, Barrier conductance accross proteins, entropy > > meters > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > https://na01.safelinks.protection.outlook.com/?url= > > http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo% > > 2Famber&data=01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da > > 82de%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=1% > > 2BHtFB0MaHN7eTwd4PvS97mzTJZXex9ilKNgWvc2Igs%3D&reserved=0 > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > https://na01.safelinks.protection.outlook.com/?url= > > http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo% > > 2Famber&data=01%7C01%7Ckoreyr%40unr.edu%7C51ed053e33494edb2c9f08d5c8da > > 82de%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=1% > > 2BHtFB0MaHN7eTwd4PvS97mzTJZXex9ilKNgWvc2Igs%3D&reserved=0 > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo% > 2Famber&data=01%7C01%7Ckoreyr%40unr.edu%7C478936f14e94496ee0b408d5cb64 > ffb2%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=0ZTGfbhxcWAf3Pg%2FA% > 2BvE0trsJgcq6%2FsCgSt7Pl6Rn7o%3D&reserved=0 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo% > 2Famber&data=01%7C01%7Ckoreyr%40unr.edu%7C478936f14e94496ee0b408d5cb64 > ffb2%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=0ZTGfbhxcWAf3Pg%2FA% > 2BvE0trsJgcq6%2FsCgSt7Pl6Rn7o%3D&reserved=0 > > > ------------------------------ > > Message: 12 > Date: Wed, 6 Jun 2018 12:08:10 +0300 > From: "Nikolay N. Kuzmich" <nnkuzmich.gmail.com> > Subject: [AMBER] Amber18 and CUDA 9.2 > To: amber.ambermd.org > Message-ID: > <CAN0UxwAa8m+NfMU2v1v3Gq8tz4Tz13eh5ieOTmFCZ913YE4_= > A.mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear Amber users and developers, > > browsing the last AMBER reflector mail I came across the topic > "Installing GPU version Amber18". > So in principle Amber18 works well with CUDA 9.2? > If the post-installations test results are OK, one can use it without > worries? > I am asking because of the troubles with installing CUDA 8.0, 9.0 and 9.1 > on my desktop with OpenSuse 15 and Ubuntu 16.04 LTS. On the contrary, CUDA > 9.2 installing was successful (at least for OpenSuse 15 and Tumbleweed). > > Thank you in advance, > Nick > > Nikolay Kuzmich > Department of Drug Safety, > Research Institute of Influenza, > WHO National Influenza Centre of Russia, > 15/17 Professor Popov St., > Saint-Petersburg > > > ------------------------------ > > Message: 13 > Date: Wed, 6 Jun 2018 17:21:10 +0800 > From: Simon Kit Sang Chu <simoncks1994.gmail.com> > Subject: [AMBER] Advanced restraints in protein mutation > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAPqeSj=uibiTn2+Mr=EVTP++eLnr3JpR+BVKN2eQzDYfC6g5jw. > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi everyone, > > I am considering a mutation by appending 4 prolines at the end of > C-terminal through FEP. Therefore, there will be disappearing hydrogen atom > in the original C-terminal and appearing tetra-proline and ions. > > To avoid the prolines appearing in the middle of protein when lambda > increases, I want to restrain the tetrapeptide close to and orient to the > C-terminal end before the transformation. The restraint should gradually > diminish as lambda goes to zero. It would be a catastrophe if the amino > acids appeared in inappropriate locations. > > To place such restraint, the most likely way is a combination of one > distance restraint between COOH and first proline residue, one angle > restraint to locate the proline center of mass to the correct end of COOH, > and one more angle restraint to point the proline open end to COOH. These > aim to facilitate shorter FEP by placing the proline in a good location and > direction. > > Is there any simpler way to restrain the tetrapeptide? Maybe combine the > first two since I am actually restraining the center of mass of the first > proline to a relative coordinate. I suspect that I would also have to > restrain the ions away from the protein? > > Regards, > Simon > > > ------------------------------ > > Message: 14 > Date: Wed, 6 Jun 2018 16:47:18 +0530 > From: Garima Singh <garimabioinfo.gmail.com> > Subject: [AMBER] Amber DSSP : Secondary structure > To: amber.ambermd.org > Message-ID: > <CAD=mwY3b616hE=doM2+4LdAJ+wz1Y03GgwMwDUx7Ks5pM62eRw. > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello Amber user, > In cpptraj command "Secstruct" has been used. Which uses dssp to calculate > secondary structure and plot were generated through gnuplot. I got this > kind of plot attached below ? > How to plot dssp.gnu visualise in ns and residue label clearly? What does > this black color represents (none) means? how to interpret it? Have you got > any idea of how to overcome this problem. > > > *Thank You and Best Wishes* > -- > *Regards* > Garima Singh > Biotechnology Division > C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division) > Central Institute Of Medicinal And Aromatic Plant > CSIR-CIMAP > Lucknow > garimabioinfo.gmail.com > > > > > *INDIA* Please don't print this e-mail unless you really need to. Be Green > ! > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: a.jpg > Type: image/jpeg > Size: 433780 bytes > Desc: not available > Url : http://lists.ambermd.org/mailman/private/amber/ > attachments/20180606/c043eeec/attachment-0001.jpg > > ------------------------------ > > Message: 15 > Date: Wed, 6 Jun 2018 08:08:02 -0400 > From: David A Case <david.case.rutgers.edu> > Subject: Re: [AMBER] Conda Installation error > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <20180606120802.3z5codglvogf2sdt.vpn-client- > 172-16-8-12.rutgers.edu> > Content-Type: text/plain; charset=us-ascii > > On Wed, Jun 06, 2018, andreas.tosstorff.cup.uni-muenchen.de wrote: > > > > I am using anaconda on Windows 10. It's still not working, also with the > > command you suggested. > > It does say on the Download Amber page (although it's a bit hidden): > "this should work for Linux and MacOS systems." As you have found, we > don't (yet) have a conda installation for Windows. > > We are in the process of testing some binary Windows installers. I > don't know enough about conda to know how hard it might be to create a > conda package. > > ....dac > > > > > ------------------------------ > > Message: 16 > Date: Wed, 6 Jun 2018 08:15:20 -0400 > From: David A Case <david.case.rutgers.edu> > Subject: Re: [AMBER] Amber18 and CUDA 9.2 > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <20180606121520.h6fe7mzznmhf62xz.vpn-client- > 172-16-8-12.rutgers.edu> > Content-Type: text/plain; charset=us-ascii > > On Wed, Jun 06, 2018, Nikolay N. Kuzmich wrote: > > > > browsing the last AMBER reflector mail I came across the topic > > "Installing GPU version Amber18". > > So in principle Amber18 works well with CUDA 9.2? > > If the post-installations test results are OK, one can use it without > > worries? > > I am asking because of the troubles with installing CUDA 8.0, 9.0 and 9.1 > > on my desktop with OpenSuse 15 and Ubuntu 16.04 LTS. On the contrary, > CUDA > > 9.2 installing was successful (at least for OpenSuse 15 and Tumbleweed). > > CUDA 9.2 seems to work fine for me on Ubunutu 18.04, but I only did the > installation a few days ago, and there is no testing beyond the test > cases. I'd certainly recommend running a short simulation on *your* > system, comparing GPU and CPU results, before starting any long > simulations. But that is good advice no matter with versions of codes > you are using. > > Note that right now, you have to edit $AMBERHOME/AmberTools/src/configure2, > > and modify the test that doesn't allow version 9.2. Once we get a little > more experience, I'll post an update to do that. > > And, please post problems if you run across them. The code in Amber18 > was frozen back in March, and we are just now testing 9.2. > > ....dac > > > > > ------------------------------ > > Message: 17 > Date: Wed, 6 Jun 2018 08:20:37 -0400 > From: Carlos Simmerling <carlos.simmerling.gmail.com> > Subject: Re: [AMBER] NaN in NEB output > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAGk3s-TbrGb_YQwZ5D=RL2ena12VRN49Qojeqj4yrS1we_EM+Q.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > These runs are not usable, something is unstable. There isn't really a > simple answer, it will depend on your system, the atom masks used, and the > initial structures. I would look at the output files for those middle > replicates and see which energy terms become large first. Also look at the > trajectory files - it is possible that the initial path generated from > using only endpoints became trapped on a path with a large barrier. You > can't always generate a good initial path just from the endpoints. Overall, > NEB is not really an automated tool and may take significant work to get it > running smoothly for a new system. > > On Wed, Jun 6, 2018 at 12:41 AM, Aravind Ravichandran <raravind.ibab.ac.in > > > wrote: > > > Dear Amber Users, > > I am performing NEB having open and close forms of the protein as the > end > > points. I had performed minimization on the structures and started > > heating the file as described in the tutorial > > (http://ambermd.org/tutorials/advanced/tutorial5_amber11/section4.htm). > > > > This was my input- > > Alanine NEB initial MD with small K > > &cntrl > > imin = 0, irest = 0, > > ntc=1, ntf=1, > > ntpr=1000, ntwx=1000, > > ntb = 0, cut = 999.0, rgbmax=999.0, > > igb = 1, saltcon=0.2, > > nstlim = 80000, nscm=0, > > dt = 0.0005, ig=-1, > > ntt = 3, gamma_ln=1000.0, > > tempi=0.0, temp0=300.0, > > tgtfitmask=":77-222.CA,N,C", > > tgtrmsmask=":1-70.CA,N,C", > > ineb = 1,skmin = 10,skmax = 10, > > nmropt=1, > > / > > &wt type='TEMP0', istep1=0,istep2=70000, > > value1=0.0, value2=300.0 > > / > > &wt type='END' > > / > > > > I created 32 replicas, with the first 16 using copies of the > > str1.inpcrd(open) and the second 16 using copies of the > > str2.inpcrd(close). > > > > I had the following values in input file- > > > > NEB replicate breakdown: > > Energy for replicate 1 = -7948.5700 > > Energy for replicate 2 = -4794.8407 > > Energy for replicate 3 = -4802.4589 > > Energy for replicate 4 = -4782.0042 > > Energy for replicate 5 = -4851.8885 > > Energy for replicate 6 = -4648.3221 > > Energy for replicate 7 = -4574.8053 > > Energy for replicate 8 = -4340.0242 > > Energy for replicate 9 = -3886.3826 > > Energy for replicate 10 = -3598.1682 > > Energy for replicate 11 = -3078.5674 > > Energy for replicate 12 = -2894.6292 > > Energy for replicate 13 = -2538.0334 > > Energy for replicate 14 = -2289.5568 > > Energy for replicate 15 = 439.5811 > > Energy for replicate 16 = NaN > > Energy for replicate 17 = NaN > > Energy for replicate 18 = 53846.6821 > > Energy for replicate 19 = 2683.6924 > > Energy for replicate 20 = -1703.6992 > > Energy for replicate 21 = -2834.8332 > > Energy for replicate 22 = -3560.3560 > > Energy for replicate 23 = -3806.8150 > > Energy for replicate 24 = -4266.6744 > > Energy for replicate 25 = -4554.9216 > > Energy for replicate 26 = -4702.1741 > > Energy for replicate 27 = -4909.6870 > > Energy for replicate 28 = -4867.9026 > > Energy for replicate 29 = -4854.1495 > > Energy for replicate 30 = -4844.1450 > > Energy for replicate 31 = -4926.5483 > > Energy for replicate 32 = -7999.0321 > > Total Energy of replicates = NaN > > > > > > Whys is there a NaN in the output file. Is it okay to have it? > > How to correct it ? > > > > > > Thank you, > > Aravind R > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > ------------------------------ > > Message: 18 > Date: Wed, 6 Jun 2018 10:10:10 -0400 > From: Ross Walker <ross.rosswalker.co.uk> > Subject: Re: [AMBER] compatibility of graphic card and Amber > To: AMBER Mailing List <amber.ambermd.org> > Cc: Zachary Fallon <zachary.fallon.stonybrook.edu> > Message-ID: <C6ECD97A-E1CA-4D21-97BF-C671BE9E23E9.rosswalker.co.uk> > Content-Type: text/plain; charset=utf-8 > > I only have 1070, 1080, 1080TI - hence why I said 'should' work. > > > On Jun 5, 2018, at 10:21 AM, Carlos Simmerling < > carlos.simmerling.gmail.com> wrote: > > > > does anyone have any actual Amber benchmark data on the 1070TI? > > > > On Tue, Jun 5, 2018 at 10:12 AM, Andrea H. Kasun < > andrea.h.kasun.gmail.com> > > wrote: > > > >> Hi Zachary, > >> > >> thank you for your response! > >> > >> Andrea > >> > >> On Tue, Jun 5, 2018 at 3:52 PM, Zachary Fallon < > >> zachary.fallon.stonybrook.edu> wrote: > >> > >>> Hi Andrea, > >>> > >>> I actually asked this question a couple days ago, Dr. Ross Walker > >>> responded quickly assuring me they should be supported -- here is a > link > >> to > >>> the post: > >>> > >>> http://archive.ambermd.org/201806/0028.html > >>> > >>> Hope this helps, > >>> > >>> --Zachary Fallon > >>> > >>> On Tue, Jun 5, 2018 at 5:25 AM, Andrea H. Kasun < > >> andrea.h.kasun.gmail.com> > >>> wrote: > >>> > >>>> Greetings, > >>>> > >>>> I am currently buying a new computer that will be used mostly for > >>>> molecular > >>>> dynamics simulations, and I need Your advice. Can You please tell me > is > >>>> graphic card Gigabyte GTX 1070 Ti compatible with Amber program > package? > >>>> > >>>> I appreciate Your help, > >>>> Andrea Hlou?ek-Kasun > >>>> _______________________________________________ > >>>> 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: 19 > Date: Wed, 6 Jun 2018 13:07:01 -0400 > From: Daniel Roe <daniel.r.roe.gmail.com> > Subject: Re: [AMBER] Amber DSSP : Secondary structure > To: AMBER Mailing List <amber.ambermd.org> > Message-ID: > <CAAC0qOaXS1nhZxYOjTvZaRwLfaOsZLycTe94WN=9TgNppYyRrA.mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > On Wed, Jun 6, 2018 at 7:17 AM, Garima Singh <garimabioinfo.gmail.com> > wrote: > > Hello Amber user, > > In cpptraj command "Secstruct" has been used. Which uses dssp to > calculate > > secondary structure and plot were generated through gnuplot. I got this > > kind of plot attached below ? > > How to plot dssp.gnu visualise in ns and residue label clearly? What > does > > You can convert to 'ns' and change the X axis label with the 'time' > and 'xlabel' keywords of the 'datafile' command, e.g. > > datafile dssp.gnu time <factor> xlabel "ns" > > where <factor> is the conversion factor from frames to ns for your > trajectory (for example if you wrote 1 frame every ps the factor would > be 0.001 to convert to ns). > > > this black color represents (none) means? how to interpret it? Have you > got > > any idea of how to overcome this problem. > > None means that the DSSP algorithm did not assign any structure. > > -Dan > > > > ------------------------------ > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > End of AMBER Digest, Vol 2314, Issue 1 > ************************************** > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jun 07 2018 - 04:00:03 PDT