Hi,
On Sat, Apr 17, 2021 at 4:01 PM waleed zalloum <waleed_zalloum.yahoo.com> wrote:
> it gives me the following error:
> Error: No 'name <modes data set name>' argument given.
The 'modes rmsip' requires both 'name' and 'name2'. So you need something like:
readdata evecs.dat name evecs
readdata evecs2.dat name evecs2
modes name evecs name2 evecs2 rmsip beg 1 end 5 out rmsip.dat setname RMSIP
If you haven't already, please read the manual entry for the 'modes'
command. Hope this helps,
-Dan
> When I specifiy the same dataset as:
> readdata evecs-ca.dat name pc1readdata evecs-ca.dat name pc2runanalysis modes rmsip name pc1 name2 pc2 beg 1 end 2 out rmsip
>
> it gives the follwing output with no error:
> INPUT: Reading Input from file pcin-emsip [readdata evecs-50-ca.dat name pc1] Reading 'evecs-ca.dat' as Evecs file with name 'pc1' Reading modes from evecs-50-ca.dat File contains 50 modes. [readdata evecs-ca.dat name pc2 ] Reading 'evecs-ca.dat' as Evecs file with name 'pc2' Reading modes from evecs-50-ca.dat File contains 50 modes. [runanalysis modes rmsip name pc1 name2 pc2 beg 1 end 2 out rmsip] ANALYZE MODES: Calculating root mean square inner product using modes from pc1, modes 1 to 2 Results are written to rmsip RMSIP calculated to modes in pc2 RMSIP= 0.999997TIME: Total analysis execution time: 0.0001 seconds.TIME: Total execution time: 0.0984 seconds.
> When I specify one dataset as follw:
> readdata evecs-ca.dat name pc1runanalysis modes rmsip name pc1 beg 1 end 2 out rmsip
>
> It gives the following error:
> INPUT: Reading Input from file pcin-emsip [readdata evecs-ca.dat name pc1] Reading 'evecs-ca.dat' as Evecs file with name 'pc1' Reading modes from evecs-ca.dat File contains 50 modes. [runanalysis modes rmsip name pc1 beg 1 end 2 out rmsip]Error: 'rmsip' requires second modes data 'name2 <modes>'TIME: Total analysis execution time: 0.0000 seconds. 1 errors encountered reading input.TIME: Total execution time: 0.0493 seconds.
>
> According to errors I got, I specified the same dataset twice.
> RMSIP needs name and name2 for the calculations. Also, according to the output RMSIP read the fifty modes in evecs-ca.dat file.
>
> This what happened.
> what is the problem?
> Thank you, indeed
>
> On Saturday, 17 April 2021, 22:00:16 EEST, amber-request.ambermd.org <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
>
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>
> 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: .rst file not produced during production run (Roberts, Amy L2)
> 2. Re: RMSIP (Daniel Roe)
> 3. Re: .rst file not produced during production run (David A Case)
> 4. Re: Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR
> (Scott Brozell)
> 5. halted quasi-harmonic MMPBSA calculation (Vaibhav Dixit)
> 6. Umbrella sampling on Amber 18 vs Amber 20 (Ramin Mehrani)
> 7. Re: Umbrella sampling on Amber 18 vs Amber 20 (David A Case)
> 8. Re: Umbrella sampling on Amber 18 vs Amber 20 (Ramin Mehrani)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 16 Apr 2021 19:04:57 +0000
> From: "Roberts, Amy L2" <AMY.ROBERTS.UCDENVER.EDU>
> Subject: Re: [AMBER] .rst file not produced during production run
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CY4PR0501MB3889941D1AE690C39A170A7A8C4C9.CY4PR0501MB3889.namprd05.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Carlos,
>
> I've attached the full file. The end of it reads:
>
> Cutoff list exceeds largest sphere in unit cell!!
> Big problems with imaging!!
> a,b,c = 24.047116319114011 22.573755462423588 27.547999941411810
> alpha,beta,gamma = 90.000000000000000 90.000000000000000 90.000000000000000
> cutlist,sphere = 11.287000000000001 11.286877731211792
>
> Thanks,
>
> Amy
>
> -----Original Message-----
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Wednesday, April 14, 2021 11:02 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] .rst file not produced during production run
>
> what did the end of the wat_md.out file say?
>
> On Wed, Apr 14, 2021 at 12:51 PM Roberts, Amy L2 <AMY.ROBERTS.ucdenver.edu>
> wrote:
>
> > Hello,
> >
> > I'm trying to simulate a box of water as part of a student lab, but am
> > finding that when I run the production step no .rst file is produced
> > as output.
> >
> > The command I am running is
> >
> > $AMBERHOME/bin/sander -O -i 4_md.in -o wat_md.out -p wat.prmtop -c
> > wat_equil.rst -r wat_md.rst -x water.mdcrd
> >
> > And the contents of my 4_md.in are
> >
> > &cntrl
> > imin = 0, irest = 1, ntx = 7,
> > ntb = 2, pres0 = 1.0, ntp = 1,
> > taup = 2.0,
> > cut = 9.287, ntr = 0,
> > ntc = 2, ntf = 2,
> > tempi = 300.0, temp0 = 300.0,
> > ntt = 3, gamma_ln = 1.0,
> > nstlim = 20000, dt = 0.001,
> > ntpr = 100, ntwx = 1, ntwr = 1000
> > /
> >
> > The minimization, defrost, and equilibration steps _seem_ to have gone
> > according to plan.
> >
> > Has anyone encountered an issue like this before? Is there additional
> > information that would be useful for troubleshooting?
> >
> > Thanks,
> >
> > Amy
> >
> > Assistant Professor of Physics
> > CU Denver | Downtown Campus
> >
> > _______________________________________________
> > 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
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>
> ------------------------------
>
> Message: 2
> Date: Fri, 16 Apr 2021 15:08:31 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] RMSIP
> Cc: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOZG621JHgNe4JMNiToYznic4xSUGubMPoE1HeX3gN+DoA.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> On Fri, Apr 16, 2021 at 11:23 AM waleed zalloum
> <waleed_zalloum.yahoo.com> wrote:
> >
> > readdata evecs-ca.dat name pc1
> > readdata evecs-ca.dat name pc2
>
> Did this give an error? You didn't specify. Assuming there is indeed
> "modes" data in evecs-ca.dat you should see a message like:
>
> Reading 'evecs-ca.dat' as Evecs file with name 'pc1'
>
> Also, you don't need to specify the same file twice. By default
> cpptraj will read all modes from the file.
>
> > runanalysis modes rmsip name pc1 name2 pc2 beg 1 end 1 out rmsip
>
> You're doing the RMSIP of eigenvector 1 to 1 which is not very useful.
> Try 'beg 1 end 2' instead.
>
> >
> >
> > Also, I projected the trajectory coordinates along pcs and got a file for this process (pca12-ca). I tried to read it instead of evecs-ca.dat in the above comman but it gave me the following error:
>
> No, this won't work. Projections are not the same as "modes" (i.e.
> eigenvectors). You can use eigenvectors to get projections, but you
> can't feed the projection values back in place of modes.
>
> Hope this helps,
>
> -Dan
>
> >
> > INPUT: Reading Input from file pcin-emsip
> > [readdata pca12-ca name pc1 ]
> > Reading 'pca12-ca' as Standard Data File with name 'pc1'
> > DataFile pca12-ca has 4 columns, 62501 lines.
> > DataFile contains labels:
> > 1: Frame
> > 2: Mode1
> > 3: Mode2
> > 4: Mode3
> > Index column is 1
> > [readdata pca12-ca name pc2]
> > Reading 'pca12-ca' as Standard Data File with name 'pc2'
> > DataFile pca12-ca has 4 columns, 62501 lines.
> > DataFile contains labels:
> > 1: Frame
> > 2: Mode1
> > 3: Mode2
> > 4: Mode3
> > Index column is 1
> > [runanalysis modes rmsip name pc1 name2 pc2 beg 1 end 1 out rmsip]
> > Error: 'pc1' not found: Modes should be read in prior to this command with 'readdata'
> >
> > TIME: Total analysis execution time: 0.0000 seconds.
> > 1 errors encountered reading input.
> > TIME: Total execution time: 0.0960 seconds.
> >
> > Also, I tried to read a file containing the first eigenvector and the other has 50 eignevector but it gave me a result of 1 as below.
> >
> > readdata evecs-firstvector-ca.dat name pc1
> > readdata evecs-allvectors-ca.dat name pc2
> > runanalysis modes rmsip name pc1 name2 pc2 beg 1 end 1 out rmsip
> >
> > I am not fully aware of what I have to do to calculate rmsip for each mode and then plot rmsip vs each mode.
> >
> > Thank you, indeed
> >
> > Waleed
> >
> > On Friday, 16 April 2021, 16:50:18 EEST, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> >
> > Hi,
> >
> > On Fri, Apr 16, 2021 at 12:01 AM waleed zalloum
> > <waleed_zalloum.yahoo.com> wrote:
> > > I tried to used modes of cpptraj, but with no succes.
> >
> >
> > Can you be more specific? What was the exact input you gave cpptraj?
> > Did you try using 'mode rmsip'? Did you get an error message?
> >
> > -Dan
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 16 Apr 2021 17:01:29 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] .rst file not produced during production run
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20210416210129.rxau2btis6vldlwv.sas1065303ec708.rad.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Fri, Apr 16, 2021, Roberts, Amy L2 wrote:
> >
> >Cutoff list exceeds largest sphere in unit cell!!
> > Big problems with imaging!!
> > a,b,c = 24.047116319114011 22.573755462423588 27.547999941411810
> > alpha,beta,gamma = 90.000000000000000 90.000000000000000 90.000000000000000
> > cutlist,sphere = 11.287000000000001 11.286877731211792
>
> You have a very small box size...very near the limit for Amber.
>
> You need to reduce your cutoff for such a small cell. I'm guessing(?) that
> you set cut=9.287 in response to earlier messages like this. But with
> constant pressure, the cell size will decrease, and with it, the largest
> value of cut that you can use.
>
> If this is "just" a student project, using the default cut of 8.0 should be
> fine for teaching. If you need to explore bigger cutoffs, you'll need to
> construct a bigger box.
>
> ....hope this helps...dac
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 16 Apr 2021 22:03:52 -0400
> From: Scott Brozell <sbrozell.comcast.net>
> Subject: Re: [AMBER] Antechamber and mol2 file with
> .<TRIPOS>UNITY_ATOM_ATTR
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20210417020352.GC17420.casegroup5.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi,
>
> 1.
> The problem with your first mol2 file is its first line which should
> be two lines, not one:
> ===
> .<TRIPOS>MOLECULE*****
> ===
>
> Note that as Dave suggested this error is caught when acdoctor mode is on:
> ===
> amber/bin/to_be_dispatched/antechamber: Fatal Error!
> No ..<TRIPOS>MOLECULE field.
> ===
>
> Note also that this error is caught by tleap:
> ===
> > loadmol2 Oplus.mol2
> Loading Mol2 file: ./Oplus.mol2
>
> Error: Invalid MOL2 format.
> Cannot find record type indicator: .<TRIPOS>MOLECULE
> ===
>
> And if that error is fixed then antechamber performs as expected.
>
> You could avoid that error by using redirection instead of cut-n-pasting:
> $ obabel -:"[O+]" -o mol2 > Oplus.mol2
>
> FWIW, antechamber is not robust with respect to file formats. It has
> long been discussed to create a bullet proof library for file I/O...
>
>
> 2.
> antechamber completely ignores record type UNITY_ATOM_ATTR and in the
> next release will so announce:
> ===
> Warning: Ignoring Mol2 record type (.<TRIPOS>UNITY_ATOM_ATTR).
> ===
>
>
> scott
>
> On Wed, Mar 31, 2021 at 08:45:28AM -0400, David A Case wrote:
> > On Wed, Mar 31, 2021, Alan wrote:
> >
> > >I'm wondering if this is a glitch or intended.
> > >
> > >Using Open Babel 3.1.0 and Antechamber 20.0:
> >
> > The design goal of antechamber is to determine Amber or GAFF atom types by
> > examining the actual geometry that is entered, pretty much ignoring any atom
> > types that might be in an input mol2 file. (This is why, for example, it
> > requires hydrogens to be present.) It was never designed to be a
> > general-purpose mol2 file interpreter.
> >
> > So, giving antechamber a "molecule" consisting of a single charged oxygen
> > atom is likely to lead it astray. Leaving out the "-dr no" flag may help in
> > deciphering what it is trying to do.
> >
> > It does sound like antehcamber might be improperly parsing a UNITY_ATOM_ATTR
> > record. I'll cc- this to Junmei Wang, who may wish to look at this. But
> > the safest thing to do is to feed antechamber a PDB-format file.
> >
> > ==========================================================================
> > >
> > >>$ obabel -:"[O+]" -o mol2
> > >.<TRIPOS>MOLECULE*****
> > > 1 0 0 0 0
> > >SMALL
> > >GASTEIGER
> > >
> > >.<TRIPOS>ATOM
> > > 1 O 0.0000 0.0000 0.0000 O.3 1 HOH1 1.0000
> > >.<TRIPOS>UNITY_ATOM_ATTR
> > >1 1
> > >charge 1
> > >.<TRIPOS>BOND
> > >1 molecule converted
> > >
> > >Putting that in file Oplus.mol2 and doing:
> > >
> > >>$ antechamber -dr no -i Oplus.mol2 -fi mol2 -o tmp -fo ac -pf y
> > >
> > >
> > >I got for tmp file:
> > >
> > >CHARGE 4.00 ( 4 )
> > >Formula: O4
> > >ATOM 1 O HOH 1 0.000 0.000 0.000 1.000000 os
> > >ATOM 2 O1 MOL 1 0.000 0.000 0.000 1.000000 os
> > >ATOM 3 O2 MOL 1 0.000 0.000 0.000 1.000000 os
> > >ATOM 4 O3 MOL 1 0.000 0.000 0.000 1.000000 os
> > >
> > >
> > >Now, if I do (add option -xu to obabel):
> > >
> > >>$ obabel -:"[O+]" -o mol2 -xu
> > >.<TRIPOS>MOLECULE
> > >*****
> > > 1 0 0 0 0
> > >SMALL
> > >GASTEIGER
> > >
> > >.<TRIPOS>ATOM
> > > 1 O 0.0000 0.0000 0.0000 O.3 1 HOH1 1.0000
> > >.<TRIPOS>BOND
> > >1 molecule converted
> > >
> > >
> > >I would get:
> > >
> > >CHARGE 1.00 ( 1 )
> > >Formula: O1
> > >ATOM 1 O HOH 1 0.000 0.000 0.000 1.000000 os
> > >
> > >
> > >Which is what I'd have expected in the first place.
> > >
> > >Here's the doce about Mol2
> > >https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fchemyang.ccnu.edu.cn%2Fccb%2Fserver%2FAIMMS%2Fmol2.pdf&data=04%7C01%7Cdavid.case%40rutgers.edu%7Cf7838f82fc894b6a9e5d08d8f41549ca%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C637527719565331758%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=UNXiXB8uAtE%2BmML8IpGe55mgX26%2BAh6IG2G37Kqx798%3D&reserved=0
> > >
> > >I'm wondering how Antechamber is dealing with .<TRIPOS>UNITY_ATOM_ATTR
> > >attribute.
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 17 Apr 2021 21:05:44 +0530
> From: Vaibhav Dixit <vaibhavadixit.gmail.com>
> Subject: [AMBER] halted quasi-harmonic MMPBSA calculation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAO6-0T=E8QmX0qRF-i5hg-ukyKZTzOej-o3igSQAySzWUyK3jQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear All,
> The standard MMPBSA calculations for a protein-protein complex went well.
> Binding energy (-8 kcal/mol) started to converge at 200 frames.
> Thus I started the quasi-harmonic (entropy=1) simulation.
> But I'm not sure if the calculation is running at all.
> I also tried with just 2 frames with the following input, but cpptraj has
> been running for more than 20 minutes with no output.
> Traj processing is still at 0 %.
> Can someone on the list please suggest how to make sure if the calculation
> is running ok? How long it can be expected to take? I have receptor and
> ligand sizes of 143 and 91 residues respectively.
>
> The prmtop files are unlikely to the source of error since the GB and PBSA
> calculations ran well with these files.
> Looking forward to valuable suggestions from the experts and users on the
> list.
> thanks and best regards
>
> The input file and command are shown below.
> mpirun -np 2 MMPBSA.py.MPI -sp ../1hga-3ner-solv.prmtop -cp
> 1hga-3ner-complex.prmtop -rp 1hga-recp1.prmtop -lp 3ner-lig1.prmtop -y ../
> 1hga-3ner-solv-prod300-reimaged.nc -i mmpbsa-quasihar.in -O -o
> FINAL-MMPBSA-RESULTS-quasihar-nf200endfr2000.dat >
> mmpbsa-quasihar-nf200endfr2000.out &
>
> (base) [exx.c107739 MMPBSA]$ more mmpbsa-quasihar.in
> Input file for running nmode and GB
> &general
> endframe=2000, verbose=2, interval=1000,
> entropy=1,
> /
> &gb
> igb=5,
>
> /
> (base) [exx.c107739 MMPBSA]$
>
> (base) [exx.c107739 MMPBSA]$ more _MMPBSA_cpptraj_entropy.out
>
> CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.09)
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 04/18/21 00:18:14
> | Available memory: 20.431 GB
>
> Reading '1hga-3ner-complex.prmtop' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> Warning: Amber topology flag 'CMAP_COUNT' is unrecognized and will be
> skipped.
> Warning: Amber topology flag 'CMAP_RESOLUTION' is unrecognized and will be
> skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_01' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_02' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_03' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_04' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_05' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_06' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_07' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_08' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_09' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_10' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_11' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_12' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_13' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_PARAMETER_14' is unrecognized and will
> be skipped.
> Warning: Amber topology flag 'CMAP_INDEX' is unrecognized and will be
> skipped.
> INPUT: Reading input from '_MMPBSA_cpptrajentropy.in'
> [trajin _MMPBSA_complex.mdcrd]
> Reading '_MMPBSA_complex.mdcrd' as Amber Trajectory
> [reference _MMPBSA_avgcomplex.pdb]
> Reading '_MMPBSA_avgcomplex.pdb' as PDB
> Setting active reference for distance-based masks:
> '_MMPBSA_avgcomplex.pdb'
> [rms mass reference :1-235]
> RMSD: (:1-235), reference is "_MMPBSA_avgcomplex.pdb:1" (:1-235),
> mass-weighted.
> Best-fit RMSD will be calculated, coords will be rotated and
> translated.
> [matrix mwcovar name comp.matrix :1-235]
> MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
> Matrix data set is 'comp.matrix'
> Start: 1 Stop: Final frame
> Mask1 is ':1-235'
> [analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce]
> Warning: The 'analyze' prefix is no longer necessary and may be soon
> deprecated.
> Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.
> Changed DataFile '_MMPBSA_complex_entropy.out' type to Evecs file
> for set Modes_00004
> DIAGMATRIX: Diagonalizing matrix comp.matrix and writing modes to
> _MMPBSA_complex_entropy.out
> Calculating all eigenvectors.
> Calculating thermodynamic data at 298.15 K, output to STDOUT
> Storing modes with name: Modes_00004
> [rms mass reference :1-143]
> RMSD: (:1-143), reference is "_MMPBSA_avgcomplex.pdb:1" (:1-143),
> mass-weighted.
> Best-fit RMSD will be calculated, coords will be rotated and
> translated.
> [matrix mwcovar name rec.matrix :1-143]
> MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
> Matrix data set is 'rec.matrix'
> Start: 1 Stop: Final frame
> Mask1 is ':1-143'
> [analyze matrix rec.matrix out _MMPBSA_receptor_entropy.out thermo reduce]
> Warning: The 'analyze' prefix is no longer necessary and may be soon
> deprecated.
> Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.
> Changed DataFile '_MMPBSA_receptor_entropy.out' type to Evecs file
> for set Modes_00007
> DIAGMATRIX: Diagonalizing matrix rec.matrix and writing modes to
> _MMPBSA_receptor_entropy.out
> Calculating all eigenvectors.
> Calculating thermodynamic data at 298.15 K, output to STDOUT
> Storing modes with name: Modes_00007
> [rms mass reference :144-235]
> RMSD: (:144-235), reference is "_MMPBSA_avgcomplex.pdb:1" (:144-235),
> mass-weighted.
> Best-fit RMSD will be calculated, coords will be rotated and
> translated.
> [matrix mwcovar name lig.matrix :144-235]
> MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
> Matrix data set is 'lig.matrix'
> Start: 1 Stop: Final frame
> Mask1 is ':144-235'
> [analyze matrix lig.matrix out _MMPBSA_ligand_entropy.out thermo reduce]
> Warning: The 'analyze' prefix is no longer necessary and may be soon
> deprecated.
> Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.
> Changed DataFile '_MMPBSA_ligand_entropy.out' type to Evecs file
> for set Modes_00010
> DIAGMATRIX: Diagonalizing matrix lig.matrix and writing modes to
> _MMPBSA_ligand_entropy.out
> Calculating all eigenvectors.
> Calculating thermodynamic data at 298.15 K, output to STDOUT
> Storing modes with name: Modes_00010
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: 1hga-3ner-complex.prmtop, 3704 atoms, 235 res, box: None, 2 mol
>
> INPUT TRAJECTORIES (1 total):
> 0: '_MMPBSA_complex.mdcrd' is an AMBER trajectory, Parm
> 1hga-3ner-complex.prmtop (reading 2 of 2)
> Coordinate processing will occur on 2 frames.
>
> REFERENCE FRAMES (1 total):
> 0: _MMPBSA_avgcomplex.pdb:1
> Active reference frame for distance-based masks is
> '_MMPBSA_avgcomplex.pdb:1'
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM '1hga-3ner-complex.prmtop' (6 actions):
> 0: [rms mass reference :1-235]
> Target mask: [:1-235](3704)
> Reference mask: [:1-235](3704)
> 1: [matrix mwcovar name comp.matrix :1-235]
> Mask [:1-235] corresponds to 3704 atoms.
> 2: [rms mass reference :1-143]
> Target mask: [:1-143](2214)
> Reference mask: [:1-143](2214)
> 3: [matrix mwcovar name rec.matrix :1-143]
> Mask [:1-143] corresponds to 2214 atoms.
> 4: [rms mass reference :144-235]
> Target mask: [:144-235](1490)
> Reference mask: [:144-235](1490)
> 5: [matrix mwcovar name lig.matrix :144-235]
> Mask [:144-235] corresponds to 1490 atoms.
> ----- _MMPBSA_complex.mdcrd (1-2, 1) -----
> 0%
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ?????????????????????????????????????????????
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
>
>
> ------------------------------
>
> Message: 6
> Date: Sat, 17 Apr 2021 11:59:56 -0400
> From: Ramin Mehrani <raminmehrani88.gmail.com>
> Subject: [AMBER] Umbrella sampling on Amber 18 vs Amber 20
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEnbn5TQ0WJ1pj8-H+2wd6fC7-4jLeUDQvTtPJo7qotEHDg-aw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
>
> I am running an umbrella sampling simulation using "colvar" namelist
> and COM_DISTANCE as the reaction coordinate to keep the distance constant
> between two chains of my protein. I notice that this method only works when
> I am using amber/18 and when I ran the exact same simulation(same input,
> initial configurations and ...) on Amber/20 the protein will get unfolded
> in an obviously wrong configuration and also the constrain distance is not
> satisfied. I should also mention that in both cases I am using GPU. I was
> wondering if there is anything that I need to change in Amber/20 to get
> similar result or the Amber/20 is not good for running umbrella sampling.
>
>
> Thanks,
> Ramin
>
>
> ------------------------------
>
> Message: 7
> Date: Sat, 17 Apr 2021 12:47:41 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Umbrella sampling on Amber 18 vs Amber 20
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20210417164741.pfohcowfyoy2wz3r.sas1065303ec708.rad.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Sat, Apr 17, 2021, Ramin Mehrani wrote:
> >
> >I am running an umbrella sampling simulation using "colvar" namelist
> >and COM_DISTANCE as the reaction coordinate to keep the distance constant
> >between two chains of my protein. I notice that this method only works when
> >I am using amber/18 and when I ran the exact same simulation(same input,
> >initial configurations and ...) on Amber/20 the protein will get unfolded
> >in an obviously wrong configuration and also the constrain distance is not
> >satisfied. I should also mention that in both cases I am using GPU. I was
> >wondering if there is anything that I need to change in Amber/20 to get
> >similar result or the Amber/20 is not good for running umbrella sampling.
>
> Can you provide a small example that illustrates the problem?
>
> ...thanks...dac
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Sat, 17 Apr 2021 13:20:32 -0400
> From: Ramin Mehrani <raminmehrani88.gmail.com>
> Subject: Re: [AMBER] Umbrella sampling on Amber 18 vs Amber 20
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEnbn5RbBbs5xcAEgAm-u2sVXC-2RAC3EjEctk5tMWWzRq-uoA.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> [image: Amber20.PNG]
>
> [image: Amber18.PNG]
> Hello,
>
> Thank you for your response, below are the snapshots of two different
> results that I am getting on Amber/18 and Amber/20 while I am using the
> exact same two attached input files. Please let me know if you need more
> specific information.
>
>
> Thanks,
> Ramin
>
> input file1:
>
>
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> pres0=1.0,
> taup=1.0,
> temp0=310.0,
> tempi=310.0,
> nstlim=1000000,
> dt=0.002,
> ntf=2,
> ntc=2,
> ntpr=50000,
> ntwx=50000,
> ntwr=50000,
> cut=10.0,
> ntb=2,
> ntp=1,
> ntt=3,
> gamma_ln=3.0,
> ig=-1,
> iwrap=1,
> infe = 1,
> /
> &pmd
> output_file = 'pmd.txt'
> output_freq = 10
> cv_file = 'cv.in'
> /
> &ewald
> skinnb=3.0,
> /
>
>
> input file2(cv.in)
> cv_file
> &colvar ! first
> cv_type = 'COM_DISTANCE'
> cv_ni =3652
> cv_i
> =1,5,7,10,13,14,15,16,17,18,20,22,25,26,27,30,31,32,33,36,39,42,44,45,46,48,50,53,55,59,63,64,65,67,69,72,75,78,81,85,86,87,89,91,94,97,100,102,109,110,111,113,115,118,120,124,128,129,130,132,134,137,139,143,147,148,149,151,153,155,159,163,164,165,166,169,172,175,177,178,179,181,184,185,186,188,190,193,196,197,198,199,200,201,203,205,208,211,212,213,214,215,216,218,220,223,224,226,228,229,233,235,237,238,239,240,242,244,247,250,251,252,253,254,255,257,259,262,263,265,267,269,271,273,274,275,277,279,282,285,286,287,288,289,290,292,294,296,300,304,305,306,308,310,312,316,318,319,320,322,324,328,329,330,332,334,337,338,340,342,344,346,348,349,350,352,354,357,358,360,362,365,367,369,370,371,373,375,378,381,384,386,393,394,395,397,400,401,402,404,406,409,412,415,417,424,425,426,428,430,433,436,437,438,441,442,443,445,447,449,453,457,458,459,461,463,466,467,469,471,473,475,477,478,479,481,483,486,489,490,491,494,495,496,498,500,503,506,507,508,511,512,513,515,517,519,523,525,526,527,529,531,533,537,540,544,545,5
46,548,550,553,555,556,557,559,561,564,566,567,568,569,572,575,578,580,581,582,584,586,589,592,593,594,595,596,597,599,602,603,604,606,608,611,613,617,621,622,623,625,627,630,633,636,638,645,646,647,649,651,654,656,660,664,665,666,668,670,672,676,680,681,682,684,687,688,689,691,693,696,698,699,700,702,704,707,710,711,712,713,714,715,717,719,721,725,729,730,731,733,736,737,738,740,742,745,746,747,748,749,750,752,754,757,760,763,765,772,773,774,776,778,780,784,786,787,788,790,792,795,797,801,805,806,807,808,811,814,817,819,820,821,823,826,827,828,830,832,835,836,838,840,841,845,847,849,850,851,852,853,856,859,862,864,865,866,868,870,872,876,880,881,882,884,886,888,892,894,895,896,898,900,903,905,909,913,914,915,916,919,922,925,927,928,929,931,933,936,937,938,939,940,941,942,945,948,951,953,954,955,957,960,961,962,964,966,969,972,973,977,978,979,981,983,986,988,989,990,992,994,997,999,1003,1007,1008,1009,1011,1013,1015,1019,1021,1022,1023,1025,1027,1030,1031,1032,1033,1034,1035,1037,1039,1042,1045,1048,1050,105
7,1058,1059,1061,1064,1065,1066,1068,1070,1072,1076,1080,1081,1082,1084,1086,1089,1092,1093,1097,1098,1099,1101,1103,1106,1108,1109,1110,1112,1114,1117,1118,1120,1122,1125,1127,1129,1130,1131,1133,1135,1137,1141,1145,1146,1147,1149,1151,1154,1157,1160,1162,1169,1170,1171,1173,1175,1178,1179,1180,1182,1184,1186,1187,1188,1190,1192,1194,1198,1202,1203,1204,1206,1208,1211,1213,1217,1221,1222,1223,1225,1227,1230,1232,1233,1234,1236,1238,1241,1243,1244,1245,1247,1249,1252,1254,1258,1262,1263,1264,1266,1269,1270,1271,1273,1276,1277,1278,1280,1283,1284,1285,1287,1289,1292,1294,1298,1302,1303,1304,1306,1308,1312,1313,1314,1316,1318,1321,1323,1327,1331,1332,1333,1335,1337,1340,1341,1343,1345,1346,1350,1352,1354,1355,1356,1357,1359,1361,1364,1367,1370,1372,1379,1380,1381,1383,1385,1389,1390,1391,1393,1396,1397,1398,1400,1402,1405,1408,1409,1410,1413,1414,1415,1417,1419,1422,1423,1425,1427,1428,1432,1434,1436,1437,1438,1439,1441,1443,1446,1448,1452,1456,1457,1458,1460,1462,1465,1466,1468,1470,1471,1475,1477,1479,1480,1
481,1482,1484,1486,1490,1491,1492,1494,1496,1499,1502,1503,1504,1507,1508,1509,1511,1513,1516,1519,1522,1524,1531,1532,1533,1535,1537,1540,1542,1546,1550,1551,1552,1554,1557,1558,1559,1561,1563,1566,1567,1568,1570,1572,1574,1575,1576,1578,1580,1583,1585,1586,1587,1589,1591,1594,1595,1596,1598,1600,1602,1603,1604,1606,1608,1610,1614,1616,1617,1618,1620,1622,1625,1626,1628,1630,1633,1635,1637,1638,1639,1641,1643,1646,1647,1649,1651,1652,1656,1658,1660,1661,1662,1663,1665,1667,1671,1672,1673,1675,1677,1679,1683,1687,1688,1689,1691,1693,1696,1698,1699,1700,1702,1704,1707,1710,1711,1712,1713,1714,1715,1717,1719,1722,1725,1726,1727,1728,1729,1730,1732,1734,1737,1739,1743,1747,1748,1749,1751,1753,1756,1758,1762,1766,1767,1768,1769,1772,1775,1778,1780,1781,1782,1784,1786,1789,1790,1791,1794,1795,1796,1798,1800,1803,1805,1806,1807,1809,1812,1813,1814,1816,1818,1821,1822,1823,1825,1827,1829,1830,1831,1833,1836,1837,1838,1839,1842,1845,1848,1850,1851,1852,1854,1856,1859,1860,1861,1862,1863,1864,1866,1869,1870,1871,1873
,1875,1878,1881,1882,1883,1884,1885,1886,1888,1890,1892,1896,1900,1901,1902,1903,1906,1909,1912,1914,1915,1916,1918,1920,1923,1926,1929,1932,1936,1937,1938,1940,1942,1945,1946,1947,1948,1949,1950,1952,1954,1957,1960,1963,1966,1970,1971,1972,1974,1976,1979,1982,1983,1984,1985,1986,1987,1989,1992,1993,1994,1996,1999,2000,2001,2003,2005,2007,2011,2015,2016,2017,2019,2021,2024,2025,2027,2029,2031,2033,2035,2036,2037,2039,2041,2044,2045,2046,2047,2048,2049,2051,2053,2056,2058,2062,2066,2067,2068,2070,2073,2074,2075,2076,2079,2082,2085,2087,2088,2089,2091,2093,2096,2097,2099,2101,2103,2105,2107,2108,2109,2111,2113,2115,2119,2122,2126,2127,2128,2130,2132,2134,2138,2142,2143,2144,2146,2148,2151,2152,2153,2154,2155,2156,2158,2160,2163,2165,2169,2173,2174,2175,2177,2179,2181,2185,2188,2192,2193,2194,2196,2198,2200,2204,2206,2207,2208,2210,2212,2215,2216,2218,2220,2222,2224,2226,2227,2228,2230,2232,2234,2238,2240,2241,2242,2244,2246,2249,2252,2253,2254,2255,2256,2257,2259,2262,2263,2264,2266,2268,2271,2273,2274,2275,22
77,2280,2281,2282,2284,2286,2289,2292,2295,2297,2304,2305,2306,2308,2310,2313,2315,2316,2317,2318,2321,2324,2327,2329,2330,2331,2333,2335,2338,2341,2344,2346,2353,2354,2355,2357,2359,2362,2363,2365,2367,2370,2372,2374,2375,2376,2378,2380,2384,2385,2386,2388,2390,2393,2395,2399,2403,2404,2405,2407,2409,2412,2413,2415,2417,2418,2422,2424,2426,2427,2428,2429,2431,2433,2436,2437,2439,2441,2443,2445,2447,2448,2449,2451,2453,2456,2458,2459,2460,2462,2464,2466,2470,2474,2475,2476,2478,2481,2482,2483,2485,2487,2490,2493,2494,2495,2496,2497,2498,2500,2502,2505,2507,2508,2509,2511,2513,2516,2517,2519,2521,2522,2526,2528,2530,2531,2532,2533,2534,2537,2540,2543,2545,2546,2547,2549,2551,2554,2557,2558,2559,2562,2563,2564,2566,2568,2571,2572,2573,2574,2575,2576,2578,2580,2583,2586,2587,2588,2591,2592,2593,2594,2597,2600,2603,2605,2606,2607,2609,2611,2614,2615,2617,2619,2620,2624,2626,2628,2629,2630,2631,2633,2635,2637,2641,2643,2644,2645,2647,2649,2652,2655,2658,2661,2665,2666,2667,2669,2671,2674,2677,2680,2682,2689,2690,
2691,2693,2695,2698,2700,2704,2708,2709,2710,2712,2714,2716,2720,2724,2725,2726,2728,2730,2733,2736,2737,2741,2742,2743,2745,2747,2749,2753,2757,2758,2759,2761,2763,2766,2769,2772,2775,2779,2780,2781,2783,2785,2787,2791,2795,2796,2797,2799,2801,2803,2807,2811,2812,2813,2814,2817,2820,2823,2825,2826,2827,2829,2831,2833,2837,2839,2840,2841,2843,2845,2848,2850,2851,2852,2854,2856,2859,2861,2865,2869,2870,2871,2873,2875,2878,2881,2884,2886,2893,2894,2895,2897,2899,2903,2904,2905,2907,2909,2912,2914,2918,2922,2923,2924,2926,2928,2930,2934,2938,2939,2940,2942,2944,2947,2950,2951,2952,2953,2954,2955,2957,2959,2962,2965,2966,2970,2971,2972,2974,2976,2980,2981,2982,2984,2986,2989,2992,2995,2997,3004,3005,3006,3008,3010,3012,3016,3020,3021,3022,3024,3027,3028,3029,3031,3034,3035,3036,3038,3040,3044,3045,3046,3048,3050,3053,3055,3056,3057,3059,3061,3064,3066,3067,3068,3070,3072,3075,3077,3081,3085,3086,3087,3089,3091,3094,3097,3098,3099,3100,3101,3102,3104,3106,3109,3110,3111,3114,3115,3116,3118,3120,3122,3126,3128,312
9,3130,3132,3134,3136,3140,3144,3145,3146,3148,3150,3153,3154,3155,3156,3157,3158,3160,3162,3165,3167,3171,3175,3176,3177,3179,3181,3184,3185,3186,3188,3190,3192,3193,3194,3196,3198,3200,3204,3207,3211,3212,3213,3215,3217,3220,3222,3223,3224,3226,3228,3231,3232,3233,3236,3237,3238,3240,3242,3245,3247,3248,3249,3251,3253,3256,3257,3258,3260,3262,3264,3265,3266,3267,3270,3273,3276,3278,3279,3280,3282,3284,3287,3289,3293,3297,3298,3299,3301,3303,3306,3308,3309,3310,3312,3314,3317,3319,3323,3327,3328,3329,3331,3333,3335,3339,3341,3342,3343,3345,3347,3350,3352,3353,3354,3356,3358,3361,3362,3363,3364,3365,3366,3368,3370,3373,3376,3377,3378,3381,3382,3383,3385,3387,3390,3391,3393,3395,3398,3400,3402,3403,3404,3406,3408,3411,3414,3417,3420,3424,3425,3426,3428,3430,3434,3435,3436,3438,3440,3443,3444,3446,3448,3451,3453,3455,3456,3457,3459,3461,3464,3466,3470,3474,3475,3476,3478,3480,3483,3486,3487,3488,3491,3492,3493,3495,3497,3500,3501,3502,3503,3504,3505,3507,3509,3512,3514,3518,3522,3523,3524,3526,3528,3530,3534,3
538,353
9,3540,3542,3544,3547,3550,3551,3552,3553,3554,3555,3557,3560,3561,3562,3564,3566,3569,3572,3573,3577,3578,3579,3581,3583,3586,3587,3588,3589,3590,3591,3593,3595,3598,3599,3601,3603,3605,3607,3609,3610,3611,3613,3615,3618,3621,3622,3623,3626,3627,3628,3630,3633,3634,3635,3636,3639,3642,3645,3647,3648,3649,3651,3654,3655,3656,3658,3660,3663,3666,3667,3668,3669,3670,3671,3673,3675,3678,3680,3681,3682,0,3683,3687,3689,3692,3695,3696,3697,3698,3699,3700,3702,3704,3707,3708,3709,3712,3713,3714,3715,3718,3721,3724,3726,3727,3728,3730,3732,3735,3737,3741,3745,3746,3747,3749,3751,3754,3757,3760,3763,3767,3768,3769,3771,3773,3776,3779,3782,3784,3791,3792,3793,3795,3797,3800,3802,3806,3810,3811,3812,3814,3816,3819,3821,3825,3829,3830,3831,3833,3835,3837,3841,3845,3846,3847,3848,3851,3854,3857,3859,3860,3861,3863,3866,3867,3868,3870,3872,3875,3878,3879,3880,3881,3882,3883,3885,3887,3890,3893,3894,3895,3896,3897,3898,3900,3902,3905,3906,3908,3910,3911,3915,3917,3919,3920,3921,3922,3924,3926,3929,3932,3933,3934,3935,3936
,3937,3939,3941,3944,3945,3947,3949,3951,3953,3955,3956,3957,3959,3961,3964,3967,3968,3969,3970,3971,3972,3974,3976,3978,3982,3986,3987,3988,3990,3992,3994,3998,4000,4001,4002,4004,4006,4010,4011,4012,4014,4016,4019,4020,4022,4024,4026,4028,4030,4031,4032,4034,4036,4039,4040,4042,4044,4047,4049,4051,4052,4053,4055,4057,4060,4063,4066,4068,4075,4076,4077,4079,4082,4083,4084,4086,4088,4091,4094,4097,4099,4106,4107,4108,4110,4112,4115,4118,4119,4120,4123,4124,4125,4127,4129,4131,4135,4139,4140,4141,4143,4145,4148,4149,4151,4153,4155,4157,4159,4160,4161,4163,4165,4168,4171,4172,4173,4176,4177,4178,4180,4182,4185,4188,4189,4190,4193,4194,4195,4197,4199,4201,4205,4207,4208,4209,4211,4213,4215,4219,4222,4226,4227,4228,4230,4232,4235,4237,4238,4239,4241,4243,4246,4248,4249,4250,4251,4254,4257,4260,4262,4263,4264,4266,4268,4271,4274,4275,4276,4277,4278,4279,4281,4284,4285,4286,4288,4290,4293,4295,4299,4303,4304,4305,4307,4309,4312,4315,4318,4320,4327,4328,4329,4331,4333,4336,4338,4342,4346,4347,4348,4350,4352,4354,43
58,4362,4363,4364,4366,4369,4370,4371,4373,4375,4378,4380,4381,4382,4384,4386,4389,4392,4393,4394,4395,4396,4397,4399,4401,4403,4407,4411,4412,4413,4415,4418,4419,4420,4422,4424,4427,4428,4429,4430,4431,4432,4434,4436,4439,4442,4445,4447,4454,4455,4456,4458,4460,4462,4466,4468,4469,4470,4472,4474,4477,4479,4483,4487,4488,4489,4490,4493,4496,4499,4501,4502,4503,4505,4508,4509,4510,4512,4514,4517,4518,4520,4522,4523,4527,4529,4531,4532,4533,4534,4535,4538,4541,4544,4546,4547,4548,4550,4552,4554,4558,4562,4563,4564,4566,4568,4570,4574,4576,4577,4578,4580,4582,4585,4587,4591,4595,4596,4597,4598,4601,4604,4607,4609,4610,4611,4613,4615,4618,4619,4620,4621,4622,4623,4624,4627,4630,4633,4635,4636,4637,4639,4642,4643,4644,4646,4648,4651,4654,4655,4659,4660,4661,4663,4665,4668,4670,4671,4672,4674,4676,4679,4681,4685,4689,4690,4691,4693,4695,4697,4701,4703,4704,4705,4707,4709,4712,4713,4714,4715,4716,4717,4719,4721,4724,4727,4730,4732,4739,4740,4741,4743,4746,4747,4748,4750,4752,4754,4758,4762,4763,4764,4766,4768,4771,
4774,4775,4779,4780,4781,4783,4785,4788,4790,4791,4792,4794,4796,4799,4800,4802,4804,4807,4809,4811,4812,4813,4815,4817,4819,4823,4827,4828,4829,4831,4833,4836,4839,4842,4844,4851,4852,4853,4855,4857,4860,4861,4862,4864,4866,4868,4869,4870,4872,4874,4876,4880,4884,4885,4886,4888,4890,4893,4895,4899,4903,4904,4905,4907,4909,4912,4914,4915,4916,4918,4920,4923,4925,4926,4927,4929,4931,4934,4936,4940,4944,4945,4946,4948,4951,4952,4953,4955,4958,4959,4960,4962,4965,4966,4967,4969,4971,4974,4976,4980,4984,4985,4986,4988,4990,4994,4995,4996,4998,5000,5003,5005,5009,5013,5014,5015,5017,5019,5022,5023,5025,5027,5028,5032,5034,5036,5037,5038,5039,5041,5043,5046,5049,5052,5054,5061,5062,5063,5065,5067,5071,5072,5073,5075,5078,5079,5080,5082,5084,5087,5090,5091,5092,5095,5096,5097,5099,5101,5104,5105,5107,5109,5110,5114,5116,5118,5119,5120,5121,5123,5125,5128,5130,5134,5138,5139,5140,5142,5144,5147,5148,5150,5152,5153,5157,5159,5161,5162,5163,5164,5166,5168,5172,5173,5174,5176,5178,5181,5184,5185,5186,5189,5190,5191,519
3,5195,5198,5201,5204,5206,5213,5214,5215,5217,5219,5222,5224,5228,5232,5233,5234,5236,5239,5240,5241,5243,5245,5248,5249,5250,5252,5254,5256,5257,5258,5260,5262,5265,5267,5268,5269,5271,5273,5276,5277,5278,5280,5282,5284,5285,5286,5288,5290,5292,5296,5298,5299,5300,5302,5304,5307,5308,5310,5312,5315,5317,5319,5320,5321,5323,5325,5328,5329,5331,5333,5334,5338,5340,5342,5343,5344,5345,5347,5349,5353,5354,5355,5357,5359,5361,5365,5369,5370,5371,5373,5375,5378,5380,5381,5382,5384,5386,5389,5392,5393,5394,5395,5396,5397,5399,5401,5404,5407,5408,5409,5410,5411,5412,5414,5416,5419,5421,5425,5429,5430,5431,5433,5435,5438,5440,5444,5448,5449,5450,5451,5454,5457,5460,5462,5463,5464,5466,5468,5471,5472,5473,5476,5477,5478,5480,5482,5485,5487,5488,5489,5491,5494,5495,5496,5498,5500,5503,5504,5505,5507,5509,5511,5512,5513,5515,5518,5519,5520,5521,5524,5527,5530,5532,5533,5534,5536,5538,5541,5542,5543,5544,5545,5546,5548,5551,5552,5553,5555,5557,5560,5563,5564,5565,5566,5567,5568,5570,5572,5574,5578,5582,5583,5584,5585,5
588,5591,5594,5596,5597,5598,5600,5602,5605,5608,5611,5614,5618,5619,5620,5622,5624,5627,5628,5629,5630,5631,5632,5634,5636,5639,5642,5645,5648,5652,5653,5654,5656,5658,5661,5664,5665,5666,5667,5668,5669,5671,5674,5675,5676,5678,5681,5682,5683,5685,5687,5689,5693,5697,5698,5699,5701,5703,5706,5707,5709,5711,5713,5715,5717,5718,5719,5721,5723,5726,5727,5728,5729,5730,5731,5733,5735,5738,5740,5744,5748,5749,5750,5752,5755,5756,5757,5758,5761,5764,5767,5769,5770,5771,5773,5775,5778,5779,5781,5783,5785,5787,5789,5790,5791,5793,5795,5797,5801,5804,5808,5809,5810,5812,5814,5816,5820,5824,5825,5826,5828,5830,5833,5834,5835,5836,5837,5838,5840,5842,5845,5847,5851,5855,5856,5857,5859,5861,5863,5867,5870,5874,5875,5876,5878,5880,5882,5886,5888,5889,5890,5892,5894,5897,5898,5900,5902,5904,5906,5908,5909,5910,5912,5914,5916,5920,5922,5923,5924,5926,5928,5931,5934,5935,5936,5937,5938,5939,5941,5944,5945,5946,5948,5950,5953,5955,5956,5957,5959,5962,5963,5964,5966,5968,5971,5974,5977,5979,5986,5987,5988,5990,5992,5995,5997
,5998,5999,6000,6003,6006,6009,6011,6012,6013,6015,6017,6020,6023,6026,6028,6035,6036,6037,6039,6041,6044,6045,6047,6049,6052,6054,6056,6057,6058,6060,6062,6066,6067,6068,6070,6072,6075,6077,6081,6085,6086,6087,6089,6091,6094,6095,6097,6099,6100,6104,6106,6108,6109,6110,6111,6113,6115,6118,6119,6121,6123,6125,6127,6129,6130,6131,6133,6135,6138,6140,6141,6142,6144,6146,6148,6152,6156,6157,6158,6160,6163,6164,6165,6167,6169,6172,6175,6176,6177,6178,6179,6180,6182,6184,6187,6189,6190,6191,6193,6195,6198,6199,6201,6203,6204,6208,6210,6212,6213,6214,6215,6216,6219,6222,6225,6227,6228,6229,6231,6233,6236,6239,6240,6241,6244,6245,6246,6248,6250,6253,6254,6255,6256,6257,6258,6260,6262,6265,6268,6269,6270,6273,6274,6275,6276,6279,6282,6285,6287,6288,6289,6291,6293,6296,6297,6299,6301,6302,6306,6308,6310,6311,6312,6313,6315,6317,6319,6323,6325,6326,6327,6329,6331,6334,6337,6340,6343,6347,6348,6349,6351,6353,6356,6359,6362,6364,6371,6372,6373,6375,6377,6380,6382,6386,6390,6391,6392,6394,6396,6398,6402,6406,6407,6408,64
10,6412,6415,6418,6419,6423,6424,6425,6427,6429,6431,6435,6439,6440,6441,6443,6445,6448,6451,6454,6457,6461,6462,6463,6465,6467,6469,6473,6477,6478,6479,6481,6483,6485,6489,6493,6494,6495,6496,6499,6502,6505,6507,6508,6509,6511,6513,6515,6519,6521,6522,6523,6525,6527,6530,6532,6533,6534,6536,6538,6541,6543,6547,6551,6552,6553,6555,6557,6560,6563,6566,6568,6575,6576,6577,6579,6581,6585,6586,6587,6589,6591,6594,6596,6600,6604,6605,6606,6608,6610,6612,6616,6620,6621,6622,6624,6626,6629,6632,6633,6634,6635,6636,6637,6639,6641,6644,6647,6648,6652,6653,6654,6656,6658,6662,6663,6664,6666,6668,6671,6674,6677,6679,6686,6687,6688,6690,6692,6694,6698,6702,6703,6704,6706,6709,6710,6711,6713,6716,6717,6718,6720,6722,6726,6727,6728,6730,6732,6735,6737,6738,6739,6741,6743,6746,6748,6749,6750,6752,6754,6757,6759,6763,6767,6768,6769,6771,6773,6776,6779,6780,6781,6782,6783,6784,6786,6788,6791,6792,6793,6796,6797,6798,6800,6802,6804,6808,6810,6811,6812,6814,6816,6818,6822,6826,6827,6828,6830,6832,6835,6836,6837,6838,6839,6840,
6842,68
44,6847,6849,6853,6857,6858,6859,6861,6863,6866,6867,6868,6870,6872,6874,6875,6876,6878,6880,6882,6886,6889,6893,6894,6895,6897,6899,6902,6904,6905,6906,6908,6910,6913,6914,6915,6918,6919,6920,6922,6924,6927,6929,6930,6931,6933,6935,6938,6939,6940,6942,6944,6946,6947,6948,6949,6952,6955,6958,6960,6961,6962,6964,6966,6969,6971,6975,6979,6980,6981,6983,6985,6988,6990,6991,6992,6994,6996,6999,7001,7005,7009,7010,7011,7013,7015,7017,7021,7023,7024,7025,7027,7029,7032,7034,7035,7036,7038,7040,7043,7044,7045,7046,7047,7048,7050,7052,7055,7058,7059,7060,7063,7064,7065,7067,7069,7072,7073,7075,7077,7080,7082,7084,7085,7086,7088,7090,7093,7096,7099,7102,7106,7107,7108,7110,7112,7116,7117,7118,7120,7122,7125,7126,7128,7130,7133,7135,7137,7138,7139,7141,7143,7146,7148,7152,7156,7157,7158,7160,7162,7165,7168,7169,7170,7173,7174,7175,7177,7179,7182,7183,7184,7185,7186,7187,7189,7191,7194,7196,7200,7204,7205,7206,7208,7210,7212,7216,7220,7221,7222,7224,7226,7229,7232,7233,7234,7235,7236,7237,7239,7242,7243,7244,7246,7248,
7251,7254,7255,7259,7260,7261,7263,7265,7268,7269,7270,7271,7272,7273,7275,7277,7280,7281,7283,7285,7287,7289,7291,7292,7293,7295,7297,7300,7303,7304,7305,7308,7309,7310,7312,7315,7316,7317,7318,7321,7324,7327,7329,7330,7331,7333,7336,7337,7338,7340,7342,7345,7348,7349,7350,7351,7352,7353,7355,7357,7360,7362,7363,7364,0
> anchor_position=-99.0,32.0,32.0,99.0
> anchor_strength = 8,8
> /
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Sat, Apr 17, 2021 at 12:47 PM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Sat, Apr 17, 2021, Ramin Mehrani wrote:
> > >
> > >I am running an umbrella sampling simulation using "colvar" namelist
> > >and COM_DISTANCE as the reaction coordinate to keep the distance constant
> > >between two chains of my protein. I notice that this method only works
> > when
> > >I am using amber/18 and when I ran the exact same simulation(same input,
> > >initial configurations and ...) on Amber/20 the protein will get unfolded
> > >in an obviously wrong configuration and also the constrain distance is not
> > >satisfied. I should also mention that in both cases I am using GPU. I was
> > >wondering if there is anything that I need to change in Amber/20 to get
> > >similar result or the Amber/20 is not good for running umbrella sampling.
> >
> > Can you provide a small example that illustrates the problem?
> >
> > ...thanks...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> ------------------------------
>
> _______________________________________________
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>
>
> End of AMBER Digest, Vol 3336, Issue 1
> **************************************
>
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Received on Fri Apr 23 2021 - 10:00:03 PDT
