Hi Mirza,
As you can see NVIDIA's cuda is not yet compatible with GCC-7. This is why Ubuntu 18 for example is not yet listed as compatible on the CUDA download page. I suggest switching to GCC / G++ / Gfortran 6. Otherwise you will not be able to build the GPU version of the code. Sometimes it's not good to be on the bleeding edge, especially in the Linux world.
All the best
Ross
> On Jul 23, 2018, at 23:50, Mirza Ahmed Hammad <hammad_mubeen.ciitsahiwal.edu.pk> wrote:
>
> Dear David Case;
>
> Yes, I had accepted to install miniconda during start of installation.
> Sorry, I had not checked 'echo $PYTHONPATH' but I had do checked that
> during './configure gnu' step, it used miniconda python. In fact during
> './configure gnu' step, it also gave warning for about lboost-thread, which
> meant boost libraries were missing, so I installed boost libraries from
> YAST package manager of Opensuse 15.0. No python variable was set
> explicitly. Amber18 installation was started just after fresh OS
> installation. I have GTX 1050Ti GPU card, I installed graphics driver
> version 390.77, as CUDA9.2 have graphics driver version 396.x so I have to
> switch back to CUDA9.1 for CUDA compatibility with graphics driver version.
> But it gave error of GCC7.x during './configure -cuda gnu' build (which
> means CUDA9.1 is not compatible with GCC7.x). I again removed all nVIDIA
> drivers properly and installed CUDA9.2 with in built driver version 396.x.
> But still there were warnings in all builds, i.e. with serial, parallel,
> and cuda builds.
>
> For me, if its not GCC7.x, then it seems that opensuse15.0 poses problems /
> conflicts about required libraries for Amber18. I re-installed Opensuse42.3
> with GCC4.8 and everything was fine again.
>
> Thanks;
>
> On 24 July 2018 at 03:00, <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. Amber targeted MD variables (??)
>> 2. Re: Amber targeted MD variables (Carlos Simmerling)
>> 3. Re: Regarding the MPI error in parallel running of 3D-RISM
>> (PRITI ROY)
>> 4. eCheminfo Oxford 3-7 Sep., Training and Innovation Course in
>> Drug Design, bursary and early-bird deadline approaching quickly
>> (Thomas Exner)
>> 5. Re: Is Amber18 compatible with GCC-7.x? (David A Case)
>> 6. Soft-core alchemical transformation in TI (Simon Kit Sang Chu)
>> 7. Re: Regarding the MPI error in parallel running of 3D-RISM
>> (David A Case)
>> 8. Re: Soft-core alchemical transformation in TI (David Cerutti)
>> 9. Re: trajout last x frames cpptraj (Daniel Roe)
>> 10. Re: Question about implicit solvation: DNA-linker conjugate
>> (Hai Nguyen)
>> 11. Re: Question about implicit solvation: DNA-linker conjugate
>> (Carlos Simmerling)
>> 12. LJEDIT syntax (Matias Machado)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 23 Jul 2018 17:57:44 +0800 (GMT+08:00)
>> From: ?? <liyao17.mails.tsinghua.edu.cn>
>> Subject: [AMBER] Amber targeted MD variables
>> To: amber <amber.ambermd.org>
>> Message-ID:
>> <57e7d81.4e83.164c692c30a.Coremail.liyao17.mails.tsinghua.edu.cn>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hello Amber users,
>>
>>
>> I'm trying to do targeted MD in Amber and have some problems in choosing
>> values of the variables, for example tgtmdfrc and restraint_wt(for
>> restraintmask). Is there any correlation between these two variables and
>> the corresponding energy terms?
>>
>>
>> Looking forward to your advices or examples or related documents
>> recommended. Thank you all!
>>
>>
>> Best,
>> Yao Li
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 23 Jul 2018 06:42:07 -0400
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Subject: Re: [AMBER] Amber targeted MD variables
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAGk3s-SP-LRWWVFmc6BSTwtyhpQJN18UNinQeVJ
>> CcGRWZd0yag.mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Restraint_wt is not used for targeted md. It goes with the positional
>> restraints with ntr=1.
>>
>> On Mon, Jul 23, 2018, 5:58 AM ?? <liyao17.mails.tsinghua.edu.cn> wrote:
>>
>>> Hello Amber users,
>>>
>>>
>>> I'm trying to do targeted MD in Amber and have some problems in choosing
>>> values of the variables, for example tgtmdfrc and restraint_wt(for
>>> restraintmask). Is there any correlation between these two variables and
>>> the corresponding energy terms?
>>>
>>>
>>> Looking forward to your advices or examples or related documents
>>> recommended. Thank you all!
>>>
>>>
>>> Best,
>>> Yao Li
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Mon, 23 Jul 2018 16:30:40 +0530
>> From: PRITI ROY <priitii.roy.gmail.com>
>> Subject: Re: [AMBER] Regarding the MPI error in parallel running of
>> 3D-RISM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAaCzDb+XVDhdKG6B3=AARTKxUp+JG=31G8HJyhfF+YSbDrm2A.mail.
>> gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Hii all,
>> Regretted for the long delay in get back to you.
>>
>> I tried my system( 5550 atoms and TIP3P) with 48 to 144 cores with many
>> type of combinations and ended up with no output for long run time
>> (~3days). I think this problem is not due to memory problem or this
>> calculation may stuck in infinite loop (might be I am wrong).
>>
>> I am sharing hardware information of our HPC which is as follows:
>>
>> 1. Master Node with Storage Node-DELL PowerEdge R730xd Server X 1
>> 2. CPU only Node - DELL Power Edge R430 Server X 6
>> 3. GPU only Node - Dell Power Edge R730 Server X 3
>> 4. 18 Ports Infiniband Switch -Mellanox SX6015 56Gb/s 18-port infiniband
>> Switch with RAIL KIT and MELLANOX passive copper cable. VPI, upto 56 Gb/s,
>> QSFP, 2M 10NOs X 1
>> 5. 24 Port Gigabit Ethernet Switch- D-link X 1
>> 6. 17 inch KVM display - ATEM/OXCA Make x 1
>> 7. 16 port KVM switch X 1
>>
>> Looking forward of your suggestions.
>>
>> Thanks,
>> Priti
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 23 Jul 2018 14:53:12 +0200
>> From: Thomas Exner <thomas.exner.uni-konstanz.de>
>> Subject: [AMBER] eCheminfo Oxford 3-7 Sep., Training and Innovation
>> Course in Drug Design, bursary and early-bird deadline approaching
>> quickly
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <4edbb598-df9e-2942-1d1f-acf24c939e92.uni-konstanz.de>
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>
>> Dear AMBER community:
>>
>> After the successful Milano workshop last week, we are now entering the
>> hot phase of preparing for the next Training and Innovation Course in
>> Drug Design taking place
>>
>> *Mon, 03. Sep. 2018 - 09:00 to Fri, 07. Sep. 2018 - 15:00*
>>
>> at *Diamond House, Harwell Science & Innovation Campus, Didcot,
>> Oxfordshire OX11 0DE, UK8*
>>
>> Besides the high-quality scientific lectures, tutorials and the time for
>> intense scientific discussions accelerating the participants' research
>> projects, the highlights of the workshop will be a tour through the
>> Diamond light source and punting in Oxford.
>>
>> For further information, please visit
>> http://www.echeminfo.com/events/echeminfo-oxford-2018 or contact us.
>>
>> Bursary Awards are available (deadline 01. August) at
>> http://www.echeminfo.com/bursary-awards
>> <https://www.researchgate.net/deref/http%3A%2F%2Fwww.
>> echeminfo.com%2Fbursary-awards>
>>
>> Early-bird reduced rates are still available until 01. August.
>>
>> Hope to see you there.
>> Thomas
>> *
>> *
>>
>> *About eChemInfo:* This series of workshops provides a set of
>> stimulating lectures and group work sessions using state-of-the-art and
>> emerging modelling techniques of relevance to chemists, life scientists
>> and modellers working in rational drug design. Participants return to
>> their labs with new ideas, best practices and software experiences to
>> maximise productivity in their own drug discovery research activities.
>>
>> Main topics covered are: virtual screening, ligand-based and
>> structure-based drug design, bio- and cheminformatics, molecular
>> dynamics simulation, drug delivery modelling, systems biology and
>> biotech drug design. The functionalities of tools developed in academic
>> groups and from the main software providers will be explored based on
>> tutorials and more important on case studies taken from ongoing research.
>>
>> Use the ?bring your own problems? option to directly apply your newly
>> acquired knowledge to your own research, profit from specific advice by
>> the experts and other participants and contribute to innovative
>> approaches for all case studies.
>>
>> Thomas Exner schrieb:
>>> Dear AMBER community:
>>> The Milano eChemInfo workshop is only two weeks away and there are still
>>> some seats available. If you are interested to join please contact me
>>> directly so that we can see what we can do to support your
>>> participation. This especially applies to participants from Italy.
>>> Best regards.
>>> Thomas
>>>
>>> Thomas Exner schrieb:
>>>> Dear all:
>>>>
>>>> Just a quick note that you can still profit from the early bird rates
>>>> until the extended deadline May 31.
>>>>
>>>> Best.
>>>> Thomas
>>>>
>>>>
>>>> Thomas Exner schrieb:
>>>>>
>>>>> eCheminfo Milano Training and Innovation Course in Drug Design
>>>>> 2018, bursary and early-bird deadline ending soon
>>>>>
>>>>> This is a short reminder that the deadlines for bursary-award
>>>>> applications and early-bird rates for the eCheminfo Training and
>>>>> Innovation Course in Drug Design, Department of Pharmaceutical
>>>>> Sciences, University of Milano, Mon, 16 Jul. to Fri, 20 Jul. 2018,
>>>>> are ending on 30 April.
>>>>>
>>>>> We are also happy to announce that the final program is available now
>> at
>>>>> http://www.echeminfo.com/events/echeminfo-euro-2018
>>>>>
>>>>> This year we feature exciting key-note talks from industry and
>> academia:
>>>>> *Rosella Ombrato, Angelini*: Novel Approaches to Drug Design and
>>>>> Development: Case Studies in Molecular Structure, Computation,
>>>>> Ligand-Receptor Interaction and Modelling*
>>>>> Roman Affentranger, Roche*: Digitalization in Pharmaceutical Research*
>>>>> Stefano Moro, University of Padova*: Recent Computational Trends in
>>>>> Exploring G Protein-Coupled Receptor (GPCR) Ligand Recognition Pathways
>>>>>
>>>>> And just to remind you on our special setup of the workshop: Use the
>>>>> ?bring your own problems? option to directly apply your newly
>>>>> acquired knowledge to your own research, and profit from specific
>>>>> advice by the experts and other participants and contribute to
>>>>> innovative approaches for all case studies. You can also present a
>>>>> poster of your work to give the other attendees an overview of your
>>>>> work and foster discussions within the groups.
>>>>>
>>>>> For further information and questions on these and other eChemInfo
>>>>> workshops, please visit http://www.echeminfo.com/events or contact us.
>>>>>
>>>>> Alessandro Contini, University of Milano (alessandro.contini.unimi.it)
>>>>> Thomas Exner, Douglas Connect (thomas.exner.uni-konstanz.de)
>>>>>
>>>>> --
>>>>> ____________________________________________________________
>> _______________________
>>>>>
>>>>> Dr. Thomas E. Exner
>>>>> Chief Scientific Officer
>>>>> Douglas Connect GmbH.
>>>>>
>>>>> www:www.douglasconnect.com
>>>>> e-mail:thomas.exner.douglasconnect.com
>>>>> phone: +49 (0)171 3807485
>>>>
>>>> --
>>>> ____________________________________________________________
>> _______________________
>>>>
>>>> Dr. Thomas E. Exner
>>>> Chief Scientific Officer
>>>> Douglas Connect GmbH.
>>>>
>>>> www:www.douglasconnect.com
>>>> e-mail:thomas.exner.douglasconnect.com
>>>> phone: +49 (0)171 3807485
>>>
>>
>>
>> --
>> ____________________________________________________________
>> _______________________
>>
>> Dr. Thomas E. Exner
>> Chief Scientific Officer
>> Douglas Connect GmbH.
>>
>> www: www.douglasconnect.com
>> e-mail: thomas.exner.douglasconnect.com
>> phone: +49 (0)171 3807485
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Mon, 23 Jul 2018 10:55:58 -0400
>> From: David A Case <david.case.rutgers.edu>
>> Subject: Re: [AMBER] Is Amber18 compatible with GCC-7.x?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <20180723145558.ckxpmndsy2jwh4qx.vpn-client-
>> 172-16-9-197.rutgers.edu>
>> Content-Type: text/plain; charset=us-ascii
>>
>> On Sat, Jul 21, 2018, Mirza Ahmed Hammad wrote:
>>
>>> I just want to ask whether AMBER18 is
>>> compatible with GCC7.x or not?
>>
>> I use gcc7 all the time, and have not seen any problems.
>>
>>> After installation for each step I tried to run tests through 'make -j4
>>> test' command, but it is always giving me error
>>>
>>> "Error: Could not import Amber Python modules!
>>> Probably your Amber Python environment was not set up correctly.
>>> We recommend adding the line:
>>> test -f ..... (sh/bash/zsh) "
>>
>> 1. Did you accept the offer to download miniconda at the configure
>> stage?
>>
>> 2. What is the result of "echo $PYTHONPATH"? Note that it is not enough
>> to have "source amber.sh" in a startup file: you have to make sure that
>> the startup file has actually been run.
>>
>> ....dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Mon, 23 Jul 2018 23:11:35 +0800
>> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
>> Subject: [AMBER] Soft-core alchemical transformation in TI
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAPqeSjm4OtMYtBDbdTAnjfr8B+x6Mh3NtK8GGGx8aa=y2rzseQ.mail.
>> gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Hi everyone,
>>
>> I am planning to transform a methanol into an ethanol. I did a simulation
>> of pure methanol solvated in water. I want to keep all the coordinates and
>> velocities, including common hydrogens, in the restart in amber format. I
>> have two concerns right now.
>>
>> First, to transform from methanol to ethanol, I have to cut a hydrogen out
>> from methanol and append a CH3- from the broken end. I briefly look into
>> AMBER manual and dummy atoms are necessary for pmemd preparation. Atoms
>> transformed must also have the same masses so I cannot transform the
>> hydrogen truncated into the new carbon. In that case, how should the
>> coordinate files be written? Can I skip creating a pdb with a crd and
>> include the hydrogens?
>>
>> Second, I am new to AMBER and I am not sure if it is using dual topology.
>> If so, the CH3- will still be bonded with methanol while having no LJ and
>> electrostatics. However, will the thermal motion created by the thermostat
>> alter the motion of methanol even at lambda = 0? If I am transforming a
>> methanol to a hexanol, the methanol motion would largely be random due to
>> the higher momentum of the "invisible" (CH2)4-CH3 tail.
>>
>> I appreciate any advice. Sorry for the long mail!
>>
>> Regards,
>> Simon
>>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Mon, 23 Jul 2018 11:50:33 -0400
>> From: David A Case <david.case.rutgers.edu>
>> Subject: Re: [AMBER] Regarding the MPI error in parallel running of
>> 3D-RISM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <20180723155033.kyxt3hlf5uccysfq.vpn-client-
>> 172-16-9-197.rutgers.edu>
>> Content-Type: text/plain; charset=us-ascii
>>
>> On Mon, Jul 23, 2018, PRITI ROY wrote:
>>>
>>> I tried my system( 5550 atoms and TIP3P) with 48 to 144 cores with many
>>> type of combinations and ended up with no output for long run time
>>> (~3days). I think this problem is not due to memory problem or this
>>> calculation may stuck in infinite loop (might be I am wrong).
>>
>> Try *much* smaller numbers of MPI threads. Use the --progress flag to
>> follow what is happening. The key point of your hardware is the amount
>> of memory, which you don't list.
>>
>> If you are able to share your PDB file, you might post it, and we can
>> see if we see problems in running this through rism3d.snglpnt. 5000
>> atoms should not require extraordinary amounts of time, such as days.
>>
>> ....hope this helps...dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Mon, 23 Jul 2018 12:57:24 -0400
>> From: David Cerutti <dscerutti.gmail.com>
>> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEmzWj0WWFLtEipFVRUAFz45BAN7OSxnHmQFOO2qd6F3VDzqzg.mail.
>> gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> There are two ways to do it:
>>
>> 1.) Map the extra dummy atoms of ethanol to methanol: in this way, each
>> atom has its exact mapped partner in methanol and ethanol, and they will
>> have exactly the same coordinates. The masses of atoms do not affect the
>> binding free energy so you don?t need to worry.
>>
>> 2.) Treat different atoms as ?softcore regions.? In this way, the
>> different atoms will move independently.
>>
>> The second way is preferred, as the result will usually be much more
>> stable.
>>
>> You can find the parameter settings in the manual (p426) and a step-by-step
>> example in http://ambermd.org/tutorials/advanced/tutorial9/index.html.
>>
>> Best of luck!
>>
>> Dave and Taisung
>>
>>
>> On Mon, Jul 23, 2018 at 11:12 AM Simon Kit Sang Chu <
>> simoncks1994.gmail.com>
>> wrote:
>>
>>> Hi everyone,
>>>
>>> I am planning to transform a methanol into an ethanol. I did a simulation
>>> of pure methanol solvated in water. I want to keep all the coordinates
>> and
>>> velocities, including common hydrogens, in the restart in amber format. I
>>> have two concerns right now.
>>>
>>> First, to transform from methanol to ethanol, I have to cut a hydrogen
>> out
>>> from methanol and append a CH3- from the broken end. I briefly look into
>>> AMBER manual and dummy atoms are necessary for pmemd preparation. Atoms
>>> transformed must also have the same masses so I cannot transform the
>>> hydrogen truncated into the new carbon. In that case, how should the
>>> coordinate files be written? Can I skip creating a pdb with a crd and
>>> include the hydrogens?
>>>
>>> Second, I am new to AMBER and I am not sure if it is using dual topology.
>>> If so, the CH3- will still be bonded with methanol while having no LJ and
>>> electrostatics. However, will the thermal motion created by the
>> thermostat
>>> alter the motion of methanol even at lambda = 0? If I am transforming a
>>> methanol to a hexanol, the methanol motion would largely be random due to
>>> the higher momentum of the "invisible" (CH2)4-CH3 tail.
>>>
>>> I appreciate any advice. Sorry for the long mail!
>>>
>>> Regards,
>>> Simon
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Mon, 23 Jul 2018 13:34:57 -0400
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] trajout last x frames cpptraj
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAC0qOZQ3Kjp_DTzM2_-JcAkR4QvmSpx=+Ow-oRmOtUFG-
>> D4yQ.mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Hi Travis,
>>
>> Just wanted to let you know that this functionality is now present in
>> cpptraj. See https://github.com/Amber-MD/cpptraj/issues/553.
>>
>> Thanks for the suggestion,
>>
>> -Dan
>>
>> On Mon, Oct 2, 2017 at 10:16 AM, Hughes, Travis
>> <travis.hughes.mso.umt.edu> wrote:
>>> Dan, Thanks for letting me know!
>>>
>>> Travis
>>>
>>> Travis Hughes
>>> Assistant Professor
>>> Biomedical and Pharmaceutical Sci.
>>> Center for Biomolecular Structure and Dynamics
>>> University of Montana, Missoula
>>> travis.hughes.umontana.edu<mailto:travis.hughes.umontana.edu>
>>> (406) 243-2750
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Oct 2, 2017, at 6:31 AM, Daniel Roe <daniel.r.roe.gmail.com<mailto:
>> daniel.r.roe.gmail.com>> wrote:
>>>
>>> Hi Travis,
>>>
>>> As has already been indicated there's currently no way to do that in
>>> cpptraj, but that's a good idea. I'll add it to my to-do list. In the
>>> meantime pytraj may be your best bet. Thanks!
>>>
>>> -Dan
>>>
>>> On Thu, Sep 28, 2017 at 2:23 PM, Hughes, Travis
>>> <travis.hughes.mso.umt.edu<mailto:travis.hughes.mso.umt.edu>> wrote:
>>> Is there any built in way (without knowing how many frames are in a
>> trajectory) to trajout only the last say 500 frames of a trajectory?
>>> for example something like this:
>>>
>>> trajin sometraj.nc 1 last 1
>>> trajout sometrajlast500.nc -500 last 1
>>>
>>>
>>> We can script something to find the length of the trajectory and then
>> use that info to do this, but is there something easy and built in to
>> cpptraj?
>>>
>>> Thanks,
>>> Travis
>>>
>>>
>>> Travis Hughes
>>> Assistant Professor
>>> Biomedical and Pharmaceutical Sci.
>>> Center for Biomolecular Structure and Dynamics
>>> University of Montana, Missoula
>>> travis.hughes.umontana.edu<mailto:travis.hughes.umontana.edu><mailto:
>> travis.hughes.umontana.edu>
>>> (406) 243-2750
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe
>>> Laboratory of Computational Biology
>>> National Institutes of Health, NHLBI
>>> 5635 Fishers Ln, Rm T900
>>> Rockville MD, 20852
>>> https://www.lobos.nih.gov/lcb
>>>
>>> _______________________________________________
>>> 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: Mon, 23 Jul 2018 14:06:32 -0400
>> From: Hai Nguyen <nhai.qn.gmail.com>
>> Subject: Re: [AMBER] Question about implicit solvation: DNA-linker
>> conjugate
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAFNMPM-9mGDV22j=q1Ljm9iROdBxX2dXxcp78f7mEd45dseuMw.mail.
>> gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> hi,
>>
>> which amber version you're using? (Just to make sure you have updated igb8
>> parameters for DNA/RNA in amber 17 or 18).
>>
>> By the way, 310K is pretty high in GB simulation (in my experience), you
>> can try with 300K.
>>
>>> The same system when simulated in explicit water remains stable and does
>> not show aggregation of the phosphates.
>>
>> How long did you run? (implicit solvent has faster sampling, so you might
>> want to run much longer explicit water to compare).
>>
>> Hai
>>
>> On Sun, Jul 22, 2018 at 2:30 PM, Supriyo Bhattacharya <sup27606.yahoo.com>
>> wrote:
>>
>>> Hi everyone,I am trying to simulate the dynamics of a linker conjugated
>>> DNA strand using implicit solvation in AMBER. The formula of the
>> molecule I
>>> am trying to simulate is:
>>> 5'GGTGCATCGATGCAGGGGGG-L-L-L-L-L-C-A-T-T-T-C-C-C-G-T-A-A-A-T-C-L-L
>>> | | |
>>> | | | | | | | | | | | | |
>>> 3'-L-L-L-L-G-T-A-A-A-G-G-G-C-
>> A-T-T-T-A-G-L-L
>>> , where L (linker) = -(PO4)-(CH2)-(CH2)-(CH2)-
>>> I have parameterized the linker using Antechamber and assigned am-bcc1
>>> charges. Next I edited the linker prepi file in xleap and specified the
>>> head and tail atoms. Finally, I created a frcmod file where I specified
>> the
>>> missing parameters (mostly the connections between L and nucleotides)
>> taken
>>> from the DNA.bsc1 parameter set. When I performed a test run using igb=8
>> at
>>> 310K, all the phosphate groups in the linker aggregated together
>>> immediately and destroyed the DNA double helix. The same system when
>>> simulated in explicit water remains stable and does not show aggregation
>> of
>>> the phosphates.
>>> Could someone with experience advise what is going wrong with the
>> implicit
>>> solvation. Do I need to set any other parameter for the linker phosphates
>>> specific to GB solvation (explicit water simulations work fine). Also,
>> the
>>> partial charges on the phosphate group are similar if not identical to
>> the
>>> DNA phosphates. The missing dihedral parameters for the linker were also
>>> taken from equivalent parameters in DNA. I am wondering whether the
>> alpha,
>>> beta and gamma parameters of IGB need to be explicitly set for the linker
>>> atoms. I thought some default reasonable values are already assigned by
>>> AMBER. Please note, I have some prior experience with GB solvent
>>> simulations in AMBER, although all of them were with pure protein
>> systems.
>>> Could somebody help?
>>> Many thanks in advance,Supriyo
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> ------------------------------
>>
>> Message: 11
>> Date: Mon, 23 Jul 2018 14:11:26 -0400
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Subject: Re: [AMBER] Question about implicit solvation: DNA-linker
>> conjugate
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAGk3s-Rp=ULzEyO6NGBqsCxQ41vrqQWMOuQTePgr6UR3B7YxyQ.mail.
>> gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Gb neck was only tested with proteins and nucleic acids, and the intrinsic
>> Born radii are optimized for those. If you create a new molecule (such as
>> your linker), you'll also want to carefully check the radii that leap
>> assigns to those atoms. They may not be appropriate. You'll probably want
>> to try to assign them by analogy rather than the guess leap takes.
>>
>> On Mon, Jul 23, 2018, 2:06 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>>
>>> hi,
>>>
>>> which amber version you're using? (Just to make sure you have updated
>> igb8
>>> parameters for DNA/RNA in amber 17 or 18).
>>>
>>> By the way, 310K is pretty high in GB simulation (in my experience), you
>>> can try with 300K.
>>>
>>>> The same system when simulated in explicit water remains stable and
>> does
>>> not show aggregation of the phosphates.
>>>
>>> How long did you run? (implicit solvent has faster sampling, so you might
>>> want to run much longer explicit water to compare).
>>>
>>> Hai
>>>
>>> On Sun, Jul 22, 2018 at 2:30 PM, Supriyo Bhattacharya <
>> sup27606.yahoo.com>
>>> wrote:
>>>
>>>> Hi everyone,I am trying to simulate the dynamics of a linker conjugated
>>>> DNA strand using implicit solvation in AMBER. The formula of the
>>> molecule I
>>>> am trying to simulate is:
>>>> 5'GGTGCATCGATGCAGGGGGG-L-L-L-L-L-C-A-T-T-T-C-C-C-G-T-A-A-A-T-C-L-L
>>>> |
>> | |
>>>> | | | | | | | | | | | | |
>>>>
>>> 3'-L-L-L-L-G-T-A-A-A-G-G-G-C-A-T-T-T-A-G-L-L
>>>> , where L (linker) = -(PO4)-(CH2)-(CH2)-(CH2)-
>>>> I have parameterized the linker using Antechamber and assigned am-bcc1
>>>> charges. Next I edited the linker prepi file in xleap and specified the
>>>> head and tail atoms. Finally, I created a frcmod file where I specified
>>> the
>>>> missing parameters (mostly the connections between L and nucleotides)
>>> taken
>>>> from the DNA.bsc1 parameter set. When I performed a test run using
>> igb=8
>>> at
>>>> 310K, all the phosphate groups in the linker aggregated together
>>>> immediately and destroyed the DNA double helix. The same system when
>>>> simulated in explicit water remains stable and does not show
>> aggregation
>>> of
>>>> the phosphates.
>>>> Could someone with experience advise what is going wrong with the
>>> implicit
>>>> solvation. Do I need to set any other parameter for the linker
>> phosphates
>>>> specific to GB solvation (explicit water simulations work fine). Also,
>>> the
>>>> partial charges on the phosphate group are similar if not identical to
>>> the
>>>> DNA phosphates. The missing dihedral parameters for the linker were
>> also
>>>> taken from equivalent parameters in DNA. I am wondering whether the
>>> alpha,
>>>> beta and gamma parameters of IGB need to be explicitly set for the
>> linker
>>>> atoms. I thought some default reasonable values are already assigned by
>>>> AMBER. Please note, I have some prior experience with GB solvent
>>>> simulations in AMBER, although all of them were with pure protein
>>> systems.
>>>> Could somebody help?
>>>> Many thanks in advance,Supriyo
>>>> _______________________________________________
>>>> 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: 12
>> Date: Mon, 23 Jul 2018 15:15:50 -0300 (UYT)
>> From: Matias Machado <mmachado.pasteur.edu.uy>
>> Subject: [AMBER] LJEDIT syntax
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <546c1d0a-a59e-44c7-81c8-120b4113008c.free.ipmont.lan>
>> Content-Type: text/plain; charset=utf-8
>>
>> Dear AMBER experts,
>>
>> I'm trying to set some Lennard-Jones interactions out-off the combination
>> rule. I was able to do it by using Parmed, however I want to set them in a
>> frcmod file so they can be applied by leap without further modification of
>> the topology.
>>
>> I know the LJEDIT section (available from amber14 on) would allow me to do
>> so, however its syntax is poorly documented, indeed I couldn't find any
>> mention to that keyword in the Amber manuals, nor in the file formats at
>> the AMBER web page [http://ambermd.org/FileFormats.php]
>>
>> The only reference I found was this post in the mailing list [
>> http://dev-archive.ambermd.org/201301/0018.html], in which its
>> implementation is discussed. From those comments, I would expect the
>> following syntax:
>>
>> LJEDIT
>> <Type 1> <Type 2> <R* pair> <Eps pair>
>> ...
>> END
>>
>> However, looking at the implementation of parm14ipq.dat [
>> https://www.ncbi.nlm.nih.gov/pubmed/25328495] and CUFIX
>> (frcmod.ff99cufix) [http://bionano.physics.illinois.edu/CUFIX]
>> I found 4 terms instead of 2 for defining the LJ interaction, my guess is
>> that 1-4 interactions can also be set separately but I'm not sure about
>> that...
>>
>> In any case... what does each set of parameters stand for?
>>
>> Best regards,
>>
>> Mat?as
>>
>> ------------------------------------
>> PhD.
>> Researcher at Biomolecular Simulations Lab.
>> Institut Pasteur de Montevideo | Uruguay
>> [http://pasteur.uy/en/laboratorios-eng/lsbm]
>> [http://www.sirahff.com]
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> End of AMBER Digest, Vol 2358, Issue 1
>> **************************************
>>
>
>
>
> --
> Mirza A. Hammad (Cell: +8613161676988)
>
> PhD Scholar
> Institute of Biophysics, UCAS
> Beijing. China
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jul 24 2018 - 08:30:02 PDT
