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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Amber16 + GTX1080 - working well (Beavil, Andrew)
> 2. Re: Error in MCPB.py (Pengfei Li)
> 3. Re: Issue with with the nocenter in tLeap (Sushil Mishra)
> 4. cpptraj analysis of water in cavity (Michael Shokhen)
> 5. Re: SHAKE Error (bharat gupta)
> 6. HYDROGEN BONDING ANALYSIS (chemjxn)
> 7. Re: Amber16 + GTX1080 - working well (Ross Walker)
> 8. Re: SHAKE Error (David A Case)
> 9. Re: HYDROGEN BONDING ANALYSIS (Hai Nguyen)
> 10. Re: cpptraj analysis of water in cavity (Daniel Roe)
> 11. Re: Issue with with the nocenter in tLeap (Daniel Roe)
> 12. How to compare protein dynamics in free and bound-ligands
> states with cpptraj (Kat G)
> 13. Re: How to compare protein dynamics in free and bound-ligands
> states with cpptraj (Adrian Roitberg)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 23 Jun 2016 20:49:26 +0000
> From: "Beavil, Andrew" <andrew.beavil.kcl.ac.uk>
> Subject: [AMBER] Amber16 + GTX1080 - working well
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <91A058CD-C78D-48B7-A607-DCFA1F3BBE97.kcl.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> I have two GTX1080s (EVGA ACX3.0) running amber and the key is to ensure
> you apply update 6, which came out last week.
> Without update 6, you will get the error : "cudaMemcpyToSymbol: SetSim
> copy to cSim failed invalid device symbol"
>
> I?m using : Amber16/Cuda8.0RC/Nvidia driver 367.27 on Centos 7
>
> it?s probably best to use ?make distclean? before running configure as
> that cleans out old half compiled junk and forces the updates to be applied.
>
> The one remaining issue I?m having is that the 367.27 driver (which is
> needed for the GTX1080s) doesn?t seem to support ?exclusive process? mode
> i.e., 'nvidia-smi -c 3? - they two cards work fine if I use ?export
> CUDA_VISIBLE_DEVICES=...'
>
> In terms of performance, for a system similar in size to the DHFR
> benchmark, running NTP MD with 2fs steps & 10A cutoff I get
> ~110 ns/day on a GTX980
> ~135ns/day on GTX980ti
> ~170ns/day on GTX1080
>
> performance drops slightly if both cards are running at the same time
> because the physically lower card heats the higher one somewhat.
> Although the performance boost is welcome, the thing I like most is that
> you can control the power usage of these cards and if I set the GTX1080 to
> 120watts, I get ~150ns/day (similar but better than the GTX980ti) for only
> half the power consumption of the GTX980ti.
> [it makes for a cooler and quieter office!]
> [the cards run at 1900MHz flat out ~165watts or 1500MHz 90watts - 120watts
> seems a sensible compromise and leads to ~1800Mhz]
>
> Does anyone have experience of the founders edition cards and are they
> better at pushing heat out of the back of the system ?
> ie less heating of neighbouring cards ?
>
> Best wishes,
>
> Andrew Beavil
>
>
> -------------------------------------------------------------------------
> Dr. Andrew J. Beavil, Phone: (+44) (0)20 78488064
> Senior Lecturer in Molecular Biophysics Fax : (+44) (0)20 78486410
>
>
>
> MRC & Asthma UK Centre in Allergic Mechanisms of Asthma
> King's College London,
> The Randall Division,
> New Hunt's House, Email: andrew.beavil.kcl.ac.uk
> <mailto:andrew.beavil.kcl.ac.uk>
> Guy's Campus,
> London Bridge,
> London. SE1 1UL
> -------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> Date: Thu, 23 Jun 2016 10:35:33 -0400
> From: Zack Scholl <zns.duke.edu<mailto:zns.duke.edu>>
> Subject: Re: [AMBER] AMBER support for gtx1080
> To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
> Message-ID:
> <CAH7kaX=e+C684h47UJh-99x624rs7pO-NVvhdW_Kd-9qEbG-Zg.mail.gmail.com
> <mailto:CAH7kaX=e+C684h47UJh-99x624rs7pO-NVvhdW_Kd-9qEbG-Zg.mail.gmail.com
> >>
> Content-Type: text/plain; charset=UTF-8
>
> In our lab we upgraded to GTX1080 from GTX980Ti and we are indeed seeing
> about 30% improvement. Make sure you have Amber16 and CUDA-8.0 (the
> developer version). Also be aware you might have to get new drivers (we're
> using RHEL 7 and the card wouldn't load on the system until we updated
> them). You can download CUDA8.0 and get the new drivers here:
> https://developer.nvidia.com/cuda-toolkit.
>
> Currently I'm a little worried something is wrong with the GTX1080 with
> AMBER16. Though it initially worked for me, it has since failed every
> simulation saying simply "cudaMemcpyToSymbol: SetSim copy to cSim failed
> invalid device symbol". Reinstalling Amber16 has not succeeded in fixing
> this error. I'd be curious if you or anyone else has run into this. I will
> try to reinstall CUDA8.0 to see if that is a possible fix, but I can't
> think of a way to reset the system beyond that (except reinstalling the OS
> I suppose!). If I keep running into this I'd probably suggest getting a
> GTX980Ti until the GTX1080 system is more stable.
> --
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 23 Jun 2016 17:51:35 -0400
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Subject: Re: [AMBER] Error in MCPB.py
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <48F1802D-A27A-4898-8F56-32FAF239C5E1.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Thanks Marcelo for the help.
>
> Hi Fabricio,
>
> The error seems relate to the atom recognition.
>
> Can you send me an independent email with your original PDB, mol2 and
> MCPB.py input file? I can help to do a check.
>
> Kind regards,
> Pengfei
>
> > On Jun 23, 2016, at 1:38 PM, Fabr?cio Bracht <fabracht1.gmail.com>
> wrote:
> >
> > Mistype...
> >
> > "MCPB.py -i Myprotein.pdb -s 1a" = "MCPB.py -i Myprotein.in -s 1a"
> >
> > 2016-06-23 14:27 GMT-03:00 Marcelo Andrade Chagas <
> andrade.mchagas.gmail.com
> >> :
> >
> >> Dear, good afternoon.
> >>
> >> At first his command is wrong from what I understand.
> >>
> >> check this first.
> >>
> >> Your .in file (not what you put into what looks like a pdb file)
> >> It must contain a type structure:
> >>
> >> MCPB.py -i 1OKL.in -s 1a
> >>
> >>
> >> [image: Imagem intercalada 1]
> >>
> >> See this appears demonstrated in the tutorial, as follows.
> >> Did you see this?
> >>
> >> [image: Imagem intercalada 2]
> >>
> >> Regards,
> >>
> >> Marcelo A. Chagas
> >>
> >> Marcelo Andrade Chagas, MSc
> >> (PhD student)
> >> Laborat?rio de Qu?mica Computacional e Modelagem Molecular - LQC-MM
> >> * http://lqcmm.qui.ufmg.br/
> >> Departamento de Qu?mica da Universidade Federal de Minas Gerais - UFMG
> >> Tel:(31)3409-5776
> >>
> >> 2016-06-23 13:19 GMT-03:00 Fabr?cio Bracht <fabracht1.gmail.com>:
> >>
> >>> Hello. I am trying to follow the MCPB.py tutorial for parameterizing
> the
> >>> metal center on an enzyme. The metal center is comprised of a Copper
> atom
> >>> bonded to 2 histidines. One of these His, is linked to the metal in a
> >>> non-standard way, so I have treated is like the LIGAND in the tutorial.
> >>> I have followed the tutorial exactly as it is, only, when I get to the
> >>> MCPB.py command "MCPB.py -i Myprotein.pdb -s 1a", I get the following
> >>> error.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> *Traceback (most recent call last): File
> >>> "/home/fabricio/amber16/bin/MCPB.py", line 562, in <module>
> premol2fs,
> >>> cutoff, watermodel, 2, largeopt, sqmopt, smchg, lgchg) File
> >>>
> >>>
> >>
> "/home/fabricio/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> >>> line 1745, in gene_model_files ionids, chargedict, lgchg, outf,
> >>> watermodel, largeopt, sqmopt) File
> >>>
> >>>
> >>
> "/home/fabricio/amber16/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> >>> line 1441, in build_large_model chargedict, IonLJParaDict, largeopt)
> >>> File
> >> "/home/fabricio/amber16/lib/python2.7/site-packages/msmtmol/gauio.py",
> >>> line 156, in write_gau_mkf chg = int(round(chargedict[ionname],
> >>> 0))KeyError: 'C'*
> >>>
> >>> What would KeyError:'C' mean?
> >>> Any help here would be nice.
> >>> Thank you
> >>> _______________________________________________
> >>> 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: 3
> Date: Fri, 24 Jun 2016 08:49:36 +0900
> From: Sushil Mishra <sushilbioinfo.gmail.com>
> Subject: Re: [AMBER] Issue with with the nocenter in tLeap
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAJ-S7c-R=
> pggZs5auuOQ8Qxu2r9Lx88N9_myVnrpdoWzTixSHw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks a lot for the new information. Does this feature align mol.rst over
> reference structure (all/nonH/backbone atoms ?) or it copies exact
> coordinates of the common part from reference structure and images rest of
> the part ? I just want to understand if tiMerge would never fail if I am
> using this procedure to generate start and end states for TI calculation.
>
> Best,
> Sushil
>
>
>
> On Fri, Jun 24, 2016 at 12:09 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > FYI cpptraj now has the ability to center coordinates on a reference
> > structure. For example, if you wanted to shift your system back to
> > your reference system:
> >
> > parm mol.parm7
> > trajin mol.rst7
> > parm system.pdb
> > reference system.pdb parm system.pdb
> > center <mask> reference
> > image !(<mask>)
> >
> > Where <mask> is the atom mask selecting the molecule you want centered.
> >
> > -Dan
> >
> >
> > On Wed, Jun 22, 2016 at 10:58 PM, Sushil Mishra <sushilbioinfo.gmail.com
> >
> > wrote:
> > > Many thanks. I was just curious if I am not doing any mistake. I needed
> > it
> > > for TI calculations in *pmemed* where I thought to keep coordinates of
> > > non-TI atoms atoms in wildtype and mutant unchanged. But there was an
> > easy
> > > workaround, and I had translated coordinates of all the mutants with
> > > respect to wild-type generated by by *tLeap*.
> > >
> > > Best,
> > > Sushil
> > >
> > >
> > > On Thu, Jun 23, 2016 at 12:22 PM, David A Case <david.case.rutgers.edu
> >
> > > wrote:
> > >
> > >> On Fri, Jun 10, 2016, Sushil Mishra wrote:
> > >> >
> > >> > source leaprc.protein.ff14SB
> > >> > source leaprc.gaff
> > >> > source leaprc.water.tip3p
> > >> > loadAmberParams frcmod.ionsjc_tip3p
> > >> > m1 = loadpdb system.pdb
> > >> >
> > >> > set default nocenter on
> > >> >
> > >> > solvateBox m1 TIP3PBOX 13
> > >> > saveamberparm m1 mol.parm7 mol.rst7
> > >> >
> > >> >
> > >> > Why the coordinates of the protein in mol.rst7 are shifted after
> > adding
> > >> > waterbox ? I am using VMD to visualize mol.rst7 and system.pdb. If I
> > do
> > >> not
> > >> > add solvent, it works as expected.
> > >>
> > >> It looks like you are correct: the "nocenter" option seems to be
> active
> > >> with
> > >> "set x box" but not with "solvateBox". Do you have a need for such
> > >> behavior?
> > >> It looks a bit tricky to implement.
> > >>
> > >> ...dac
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 24 Jun 2016 07:58:04 +0000
> From: Michael Shokhen <michael.shokhen.biu.ac.il>
> Subject: [AMBER] cpptraj analysis of water in cavity
> To: "AMBER.ambermd.org" <AMBER.ambermd.org>
> Message-ID:
> <
> AM3PR04MB0565D1A35C1C6A39C23F37C5B62E0.AM3PR04MB0565.eurprd04.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Amber experts,
>
> I know how to write cpptraj command for measuring over all productive MD
> simulation frames the distance between any two residues with fixed
> specified
> numbers as for instance between Ser10 and Wat 1000:
>
> distance res10_wat1000 :10.OG :1000.O out dist_res10_wat1000.agr
>
> I need now to analyze a possibility of bulk water molecules diffusion
> during MD simulation into and out the cavity inside protein
> and H-bond formation with Ser 10 residue located there.
> By the logic, I should identify in every MD frame the water molecule
> located at that instant time in a minimal inter-atomic distance
> between OG atom of Ser 10 and O atom of this water molecule.
> The measured distances must be saved in a file like
> dist_res10_wat_in_cavity.agr.
>
> I don't know how to modify the cpptraj command above to be relevant for
> the described
> water diffusion analysis.
>
> I would appreciate your help in correct formulation of the cpptraj command.
>
> Thank you,
> Michael
>
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<
> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 24 Jun 2016 19:42:55 +0900
> From: bharat gupta <bharat.85.monu.gmail.com>
> Subject: Re: [AMBER] SHAKE Error
> To: amber.ambermd.org
> Message-ID:
> <
> CAAh+zSVmEv4Wt5Dc3SOYxEjOnnV_KojBZYkmOy5SC5hgLXirTQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
> I am performing a simulation of a docked complex of
> protein-ligand(cellotriose) using AMBER12. For the initial settings such as
> minimization and equilibration I am following this tutorial :
> http://www.ii.uib.no/~slars/bioinfocourse/PDFs/amber_tutorial.pdf. I
> prepared the ligand using GLYCAM_06 forcefield and for protein I used
> ff99SB. While running the equilibration step, I am getting the following
> error:
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 392 803 804
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> After looking into the list, I found that there might be some problem with
> my system. But, I viewed the system in Pymol and everything looked fine to
> me. I have attached all the .out file here:
> https://drive.google.com/open?id=0B6ehLXK0eP7sYVZKd1FCUjk2VmM
>
> Could anybody tell me what is going wrong with the system?
>
>
> --
> *Best Regards*
> BM
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 24 Jun 2016 19:35:19 +0800 (CST)
> From: chemjxn <chemjxn.126.com>
> Subject: [AMBER] HYDROGEN BONDING ANALYSIS
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID: <12c3fdcb.c4b1.1558231570a.Coremail.chemjxn.126.com>
> Content-Type: text/plain; charset="gbk"
>
> Dear Sir/Madam:
>
> I apply MD simulation to investigate fXa which is a protein-ligand
> complex. I got the result file. When analyzing the results, I have some
> problems. I want to use AMBER14 program do hydrogen bonding analysis, but
> there exist some error, as shown in the following:
>
> Error: 'donor' is deprecated.
>
> Hydrogen bond acceptors and donors are defined within the 'hbond'
> action.
>
> Error: Unrecognized character in expression: :
>
> 'donor mask :GLN.OE1': Invalid command or expression.
>
> 1 errors encountered reading input.
> command: cpptraj complex.top < analyse_hbond.ptraj > analyse_hbond.out. I
> use the ptraj script named analyse_hbond.ptraj (see appendix). I hope for
> an early answer to my question. Thank you!
>
> Sincerely,
>
> Liyan
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 7
> Date: Fri, 24 Jun 2016 07:11:50 -0600
> From: Ross Walker <rosscwalker.gmail.com>
> Subject: Re: [AMBER] Amber16 + GTX1080 - working well
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <i7943nrkj6e66a3qa723cd38.1466773572838.email.android.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi Andrew
> The card you.mention looks like it is reference <cough>founders </cough>
> design already. I recommend only ever using such cards. The overstocked
> multi fan systems are fine for games but unreliable for cuda apps and the
> things like the 3 fan designs they have are terrible in multi-task
> configuration. It also helps to use server cases with ducted cooling - e.g.
> 2 U boxes like this
> http://exxactcorp.com/index.php/solution/solu_detail/201
> This clocks down a whole lot less than desktop boxes.
> You can set cool bits in your xorg.conf file and set the fans to 100% this
> stops things clocking down as well in multi gpu configuration but your
> system will sound like a bunch of jet engines in a box.
> Didn't know about the exclusive mode not working. Yet another big. I'll
> check it an file with nvidia. They rushed out the gtx1080 3 months before
> it was ready so it is still massively experimental. At least they fixed the
> fact it was getting incorrect numerical results (4th time now /fail)
> quickly with the 367.27 driver. But the fact you have to get a release
> candidate of the Cuda compiler to use the card at launch is just freaking
> ridiculous.
> All the bestRoss
> -------- Original message --------From: "Beavil, Andrew" <
> andrew.beavil.kcl.ac.uk> Date: 6/23/16 14:49 (GMT-07:00) To:
> amber.ambermd.org Subject: [AMBER] Amber16 + GTX1080 - working well
> I have two GTX1080s (EVGA ACX3.0) running amber and the key is to ensure
> you apply update 6, which came out last week.
> Without update 6, you will get the error : "cudaMemcpyToSymbol: SetSim
> copy to cSim failed invalid device symbol"
>
> I?m using : Amber16/Cuda8.0RC/Nvidia driver 367.27 on Centos 7
>
> it?s probably best to use ?make distclean? before running configure as
> that cleans out old half compiled junk and forces the updates to be applied.
>
> The one remaining issue I?m having is that the 367.27 driver (which is
> needed for the GTX1080s) doesn?t seem to support ?exclusive process? mode
> i.e., 'nvidia-smi -c 3?? - they two cards work fine if I use ?export
> CUDA_VISIBLE_DEVICES=...'
>
> In terms of performance, for a system similar in size to the DHFR
> benchmark, running NTP MD with 2fs steps & 10A cutoff I get
> ~110 ns/day on a GTX980
> ~135ns/day on GTX980ti
> ~170ns/day on GTX1080
>
> performance drops slightly if both cards are running at the same time
> because the physically lower card heats the higher one somewhat.
> Although the performance boost is welcome, the thing I like most is that
> you can control the power usage of these cards and if I set the GTX1080 to
> 120watts, I get ~150ns/day (similar but better than the GTX980ti) for only
> half the power consumption of the GTX980ti.
> [it makes for a cooler and quieter office!]
> [the cards run at 1900MHz flat out ~165watts or 1500MHz 90watts - 120watts
> seems a sensible compromise and leads to ~1800Mhz]
>
> Does anyone have experience of the founders edition cards and are they
> better at pushing heat out of the back of the system ?
> ie less heating of neighbouring cards ?
>
> Best wishes,
>
> Andrew Beavil
>
>
> -------------------------------------------------------------------------
> Dr. Andrew J. Beavil,??????????????????????? Phone: (+44) (0)20 78488064
> Senior Lecturer in Molecular Biophysics????? Fax? : (+44) (0)20 78486410
>
>
>
> MRC & Asthma UK Centre in Allergic Mechanisms of Asthma
> King's College London,
> The Randall Division,
> New Hunt's House,???????????????????????? Email: andrew.beavil.kcl.ac.uk
> <mailto:andrew.beavil.kcl.ac.uk>
> Guy's Campus,
> London Bridge,
> London. SE1 1UL
> -------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> Date: Thu, 23 Jun 2016 10:35:33 -0400
> From: Zack Scholl <zns.duke.edu<mailto:zns.duke.edu>>
> Subject: Re: [AMBER] AMBER support for gtx1080
> To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
> Message-ID:
> <CAH7kaX=e+C684h47UJh-99x624rs7pO-NVvhdW_Kd-9qEbG-Zg.mail.gmail.com
> <mailto:CAH7kaX=e+C684h47UJh-99x624rs7pO-NVvhdW_Kd-9qEbG-Zg.mail.gmail.com
> >>
> Content-Type: text/plain; charset=UTF-8
>
> In our lab we upgraded to GTX1080 from GTX980Ti and we are indeed seeing
> about 30% improvement. Make sure you have Amber16 and CUDA-8.0 (the
> developer version). Also be aware you might have to get new drivers (we're
> using RHEL 7 and the card wouldn't load on the system until we updated
> them). You can download CUDA8.0 and get the new drivers here:
> https://developer.nvidia.com/cuda-toolkit.
>
> Currently I'm a little worried something is wrong with the GTX1080 with
> AMBER16. Though it initially worked for me, it has since failed every
> simulation saying simply "cudaMemcpyToSymbol: SetSim copy to cSim failed
> invalid device symbol". Reinstalling Amber16 has not succeeded in fixing
> this error. I'd be curious if you or anyone else has run into this. I will
> try to reinstall CUDA8.0 to see if that is a possible fix, but I can't
> think of a way to reset the system beyond that (except reinstalling the OS
> I suppose!). If I keep running into this I'd probably suggest getting a
> GTX980Ti until the GTX1080 system is more stable.
> --
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> ------------------------------
>
> Message: 8
> Date: Fri, 24 Jun 2016 09:38:46 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] SHAKE Error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20160624133846.GA32457.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Fri, Jun 24, 2016, bharat gupta wrote:
>
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 2 392 803 804
>
> The problem is at atoms 803 and 804. Check your structure carefully at
> that point.
>
> You might also try a minimization without SHAKE, then continue with
> equilibration using SHAKE.
>
> ...dac
>
>
Hi,
Thank you for your response. I looked at the pdb file and atoms 803 and 804
are O and H, respectively of a water molecule. I initially did the
minimization without SHAKE. Here's the minimization parameters for
ions+solvent and entire system (separately):
min_sol.in
Minimization of waters
&cntrl
imin=1, maxcyc=10000,
ncyc=5000, ntb=1,
cut=10, ntpr=5,
ntr=1,
restraint_wt=2.0
&end
Group input for restrained atoms
100.0
RES 1 535
END
END
min_all.in
minimization of the whole system
&cntrl
imin = 1,
maxcyc=10000, ncyc=7000,
ntb=1, cut=10, ntpr=5,
&end
other parameters for heat, density and equilibration are the same as used
in Ross's tutorial.
Could you please tell me where am I going wrong?
Moreover, I am also following the protein-ligand tutorial from Rizzo lab (
http://ringo.ams.sunysb.edu/index.php/2013_AMBER_Tutorial_with_UMP_and_OMP#Equilibration),
where after minimization, equlibration is done at certain temperature and
then 3 rounds of minimization again with different restraint wts. When I
looked at the system after the first equilibration, I found that protein
moved out of the water box. Is this okay, as I am not getting an error for
the subsequent minimization steps, even though the protein is outside the
solvent box?
I also found that there was not heating of the system and density
equilibration, as mentioned in the Ross tutorial (
http://www.ii.uib.no/~slars/bioinfocourse/PDFs/amber_tutorial.pdf), is this
okay?
Regards
BM
>
> ------------------------------
>
> Message: 9
> Date: Fri, 24 Jun 2016 10:41:38 -0400
> From: Hai Nguyen <nhai.qn.gmail.com>
> Subject: Re: [AMBER] HYDROGEN BONDING ANALYSIS
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAFNMPM9VY2gwhej6qPFpA8stJz-R3Ewweaq5gxsrWZgfgWXs9w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi
>
> you don't need to explicitly specify donor and acceptor anymore.
>
> Please read this hbond tutorial:
> http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/
>
> Hai
>
> On Fri, Jun 24, 2016 at 7:35 AM, chemjxn <chemjxn.126.com> wrote:
>
> > Dear Sir/Madam:
> >
> > I apply MD simulation to investigate fXa which is a protein-ligand
> > complex. I got the result file. When analyzing the results, I have some
> > problems. I want to use AMBER14 program do hydrogen bonding analysis, but
> > there exist some error, as shown in the following:
> >
> > Error: 'donor' is deprecated.
> >
> > Hydrogen bond acceptors and donors are defined within the 'hbond'
> > action.
> >
> > Error: Unrecognized character in expression: :
> >
> > 'donor mask :GLN.OE1': Invalid command or expression.
> >
> > 1 errors encountered reading input.
> > command: cpptraj complex.top < analyse_hbond.ptraj > analyse_hbond.out.
> I
> > use the ptraj script named analyse_hbond.ptraj (see appendix). I hope for
> > an early answer to my question. Thank you!
> >
> > Sincerely,
> >
> > Liyan
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> ------------------------------
>
> Message: 10
> Date: Fri, 24 Jun 2016 11:31:49 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] cpptraj analysis of water in cavity
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAAC0qObeCCCxaManRiFnKQe0cZcCHLZit2Rz0p6NNp3KiwCC8g.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Probably as a starting point you'll want to look at solute-solvent
> hydrogen bonding between your serine and water. Something like:
>
> hbond Ser10 out nhbvtime.dat :10 avgout UU.dat \
> solventdonor :WAT solventacceptor :WAT.O \
> solvout UV.dat bridgeout Bridge.dat
>
> should be enough to get you started. Consult the manual for more
> details on the 'hbond' command.
>
> -Dan
>
>
> On Fri, Jun 24, 2016 at 1:58 AM, Michael Shokhen
> <michael.shokhen.biu.ac.il> wrote:
> > Dear Amber experts,
> >
> > I know how to write cpptraj command for measuring over all productive MD
> > simulation frames the distance between any two residues with fixed
> specified
> > numbers as for instance between Ser10 and Wat 1000:
> >
> > distance res10_wat1000 :10.OG :1000.O out dist_res10_wat1000.agr
> >
> > I need now to analyze a possibility of bulk water molecules diffusion
> > during MD simulation into and out the cavity inside protein
> > and H-bond formation with Ser 10 residue located there.
> > By the logic, I should identify in every MD frame the water molecule
> > located at that instant time in a minimal inter-atomic distance
> > between OG atom of Ser 10 and O atom of this water molecule.
> > The measured distances must be saved in a file like
> dist_res10_wat_in_cavity.agr.
> >
> > I don't know how to modify the cpptraj command above to be relevant for
> the described
> > water diffusion analysis.
> >
> > I would appreciate your help in correct formulation of the cpptraj
> command.
> >
> > Thank you,
> > Michael
> >
> >
> >
> >
> >
> > *****************************
> > Michael Shokhen, PhD
> > Associate Professor
> > Department of Chemistry
> > Bar Ilan University,
> > Ramat Gan, 52900
> > Israel
> > email: shokhen.mail.biu.ac.il<
> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
>
> ------------------------------
>
> Message: 11
> Date: Fri, 24 Jun 2016 11:33:47 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Issue with with the nocenter in tLeap
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qObGHjrh-A4C=094jo35kjm9j77kD0N_+ztv=
> E8-5y+kng.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> The 'center' command will not perform any alignment beyond
> translation, but I think that should be enough since I don't think
> LEaP will do any rotation of coordinates (others please correct me if
> I'm wrong here). The alignment will use whatever mask you give it, so
> if you specify ':1' it will center residue 1 in your input trajectory
> on residue in the reference, etc.
>
> -Dan
>
> On Thu, Jun 23, 2016 at 5:49 PM, Sushil Mishra <sushilbioinfo.gmail.com>
> wrote:
> > Thanks a lot for the new information. Does this feature align mol.rst
> over
> > reference structure (all/nonH/backbone atoms ?) or it copies exact
> > coordinates of the common part from reference structure and images rest
> of
> > the part ? I just want to understand if tiMerge would never fail if I am
> > using this procedure to generate start and end states for TI calculation.
> >
> > Best,
> > Sushil
> >
> >
> >
> > On Fri, Jun 24, 2016 at 12:09 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> FYI cpptraj now has the ability to center coordinates on a reference
> >> structure. For example, if you wanted to shift your system back to
> >> your reference system:
> >>
> >> parm mol.parm7
> >> trajin mol.rst7
> >> parm system.pdb
> >> reference system.pdb parm system.pdb
> >> center <mask> reference
> >> image !(<mask>)
> >>
> >> Where <mask> is the atom mask selecting the molecule you want centered.
> >>
> >> -Dan
> >>
> >>
> >> On Wed, Jun 22, 2016 at 10:58 PM, Sushil Mishra <
> sushilbioinfo.gmail.com>
> >> wrote:
> >> > Many thanks. I was just curious if I am not doing any mistake. I
> needed
> >> it
> >> > for TI calculations in *pmemed* where I thought to keep coordinates of
> >> > non-TI atoms atoms in wildtype and mutant unchanged. But there was an
> >> easy
> >> > workaround, and I had translated coordinates of all the mutants with
> >> > respect to wild-type generated by by *tLeap*.
> >> >
> >> > Best,
> >> > Sushil
> >> >
> >> >
> >> > On Thu, Jun 23, 2016 at 12:22 PM, David A Case <
> david.case.rutgers.edu>
> >> > wrote:
> >> >
> >> >> On Fri, Jun 10, 2016, Sushil Mishra wrote:
> >> >> >
> >> >> > source leaprc.protein.ff14SB
> >> >> > source leaprc.gaff
> >> >> > source leaprc.water.tip3p
> >> >> > loadAmberParams frcmod.ionsjc_tip3p
> >> >> > m1 = loadpdb system.pdb
> >> >> >
> >> >> > set default nocenter on
> >> >> >
> >> >> > solvateBox m1 TIP3PBOX 13
> >> >> > saveamberparm m1 mol.parm7 mol.rst7
> >> >> >
> >> >> >
> >> >> > Why the coordinates of the protein in mol.rst7 are shifted after
> >> adding
> >> >> > waterbox ? I am using VMD to visualize mol.rst7 and system.pdb. If
> I
> >> do
> >> >> not
> >> >> > add solvent, it works as expected.
> >> >>
> >> >> It looks like you are correct: the "nocenter" option seems to be
> active
> >> >> with
> >> >> "set x box" but not with "solvateBox". Do you have a need for such
> >> >> behavior?
> >> >> It looks a bit tricky to implement.
> >> >>
> >> >> ...dac
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
>
> ------------------------------
>
> Message: 12
> Date: Fri, 24 Jun 2016 13:38:37 -0500
> From: Kat G <katwin86.gmail.com>
> Subject: [AMBER] How to compare protein dynamics in free and
> bound-ligands states with cpptraj
> To: amber.ambermd.org
> Message-ID:
> <CAAoPRXU=
> j0Do143zL7V5-6w0ZSVM9LXC+_P6m_aK7Jdi8HZ-Gg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all,
>
> I am using PCA to highlight concerted motions different when protein is
> free and bound with many ligands. Projections of individual trajectories on
> the first several PCs calculated from combined trajectories are
> significantly different. Then how can I trace back to each trajectory to
> see which residues in each system contribute to motions in those combined
> PCs.
>
> Could you please show me how to apply PCA and cluster analysis to
> investigate changes in dynamics of protein when unbound and bound with
> different ligands. In some references for the use of PCA and cluster
> analysis, the purpose of those studies is to prove for convergence, rather
> than analyzing the differences among trajectories. I tried to follow the
> study from this paper
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300347/pdf/10388775.pdf, but
> still confused of what they did and what cpptraj can calculate.
>
> Thanks for any suggestion.
>
>
> ------------------------------
>
> Message: 13
> Date: Fri, 24 Jun 2016 14:42:54 -0400
> From: Adrian Roitberg <roitberg.ufl.edu>
> Subject: Re: [AMBER] How to compare protein dynamics in free and
> bound-ligands states with cpptraj
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <19db81cc-9409-356a-0fef-e585683819cb.ufl.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi Kat
>
> You can take a look at
>
> "New insights into the meaning and usefulness of principal component
> analysis of concatenated trajectories"doi:10.1002/jcc.23811Authors
> Gustavo Pierdominici-Sottile,, Juliana Palma
>
> and
>
> On the analysis and comparison of conformer-specific essential dynamics
> upon ligand binding to a protein Grosso, M.; Kalstein, A.; Parisi, G.;
> Roitberg, A. E.; Fernandez-Alberti, S. J. Chem. Phys. 142, 245101. (2015)
>
>
> Cheers
>
> adrian
>
>
>
> On 6/24/16 2:38 PM, Kat G wrote:
> > Hi all,
> >
> > I am using PCA to highlight concerted motions different when protein is
> > free and bound with many ligands. Projections of individual trajectories
> on
> > the first several PCs calculated from combined trajectories are
> > significantly different. Then how can I trace back to each trajectory to
> > see which residues in each system contribute to motions in those combined
> > PCs.
> >
> > Could you please show me how to apply PCA and cluster analysis to
> > investigate changes in dynamics of protein when unbound and bound with
> > different ligands. In some references for the use of PCA and cluster
> > analysis, the purpose of those studies is to prove for convergence,
> rather
> > than analyzing the differences among trajectories. I tried to follow the
> > study from this paper
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300347/pdf/10388775.pdf,
> but
> > still confused of what they did and what cpptraj can calculate.
> >
> > Thanks for any suggestion.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1616, Issue 1
> **************************************
>
>
--
*Best Regards*
Bharat
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jun 26 2016 - 08:30:03 PDT
