Re: [AMBER] AMBER Digest, Vol 1169, Issue 1

From: Arjun Sharma <arjunsharma83.gmail.com>
Date: Wed, 25 Mar 2015 16:54:31 -0500

Dear Dr. Swails,

Thanks for the insight. I guess it is not as straight forward as I though it was. But I want to go ahead with it. I would greatly appreciate some timely suggestions from your side as I go through the process of getting parameters and reference energies for my organic polymers do some experimentations. I will keep you posted if thatís fine with you and hopefully some inputs from your side during each work process could save me some time.

Thanks,
Ashar

On Mar 25, 2015, at 2:00 PM, amber-request.ambermd.org wrote:

>
>
> Message: 4
> Date: Tue, 24 Mar 2015 21:36:02 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] CpHMD-pHREX AMBER14
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qmgyopMOjKTSS0E2io7E9KBTGk2tYNeX0jB0yBoDWOKA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Tue, Mar 24, 2015 at 1:37 PM, Arjun Sharma <arjunsharma83.gmail.com>
> wrote:
>
>> Dear Amber users,
>>
>> I?m wondering if it is possible to run CpHMD-pHREX in AMBER 14 for the
>> organic polymer with -COOH functional group. I see that leaprc.constph is
>> mostly set up for amino acids and since I am dealing with non-standard
>> residues , how do I go about it ?
>>
>
> ?This is a more challenging problem than it may at first appear. Basically
> what you need to do is define the charge vectors for each of the
> protonation states that you want to allow your new titratable residue to
> have access to. Then, you need to compute the reference energy, which is
> the energy at which some model compound titrates to the *correct*
> experimental pKa.
>
> So you need a representative compound for which you know an experimental
> pKa, you need to estimate its reference energy (thermodynamic integration
> will often get you either the correct reference energy or it will get you
> very close). Then you need to run a titration of your model compound to
> make sure that the computed pKa matches the target pKa. If it doesn't, you
> need to adjust your reference energy so that it does.
>
> This is a very basic overview of what needs to be done. Going into the
> specifics, giving you a step-by-step workflow to implement it yourself
> would take me too long to put it into an email, so you will need to do a
> lot of the legwork yourself. I suggest starting with Mongan's original
> paper, read a couple of mine and Adrian's, read the Amber manual chapter on
> constant pH MD (which briefly describes the steps necessary to create your
> own titratable residue), read the code if such things help you understand
> stuff, and most importantly, experiment and try things out.
>
> Note that I spent the 5 years of my graduate career on this method. As a
> novice to Amber and the field in general when I started, it took me the
> better part of a year to understand the finer details of the method, and
> closer to 2 until I got to the point where I was able to implement the
> explicit solvent model and develop a rigorous workflow to parametrize new
> residues (or reparametrize existing residues for new solvent models). I
> had some scripts that would automate parts of the workflow, but for the
> most part I did it by hand to make sure at each step that everything was
> correct. Was I not new to the field at the start (but just new to CpHMD),
> it would not have taken as long; but I don't know how long it would have
> taken me in that case.
>
> I'm not trying to discourage you from pursuing this (quite the opposite!),
> but I want to stress that this task is *not* simple and could require a
> substantial time investment to implement. (And if you do, I would
> encourage you to contribute the parameters for the new residue you
> parametrized back to Amber so others can benefit from---and cite---your
> work).
>
> HTH,
> Jason
>
>
> Any help is appreciated.
>>
>> Thanks,
>> Ashar
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 25 Mar 2015 09:40:20 +0800 (GMT+08:00)
> From: ?? <whlei.hust.edu.cn>
> Subject: [AMBER] The unperturbed charge of the unit: -2.980000 is not
> integral
> To: amber.ambermd.org
> Message-ID: <a63ab8.42e6.14c4e96612f.Coremail.whlei.hust.edu.cn>
> Content-Type: text/plain; charset=GBK
>
> Dear amber users,
>
> i generate a protein complex (protein and ligand) by autodock adding polar charges.when i did simulation,it came with a error: "The unperturbed charge of the unit: -2.980000 is not integral". and then i can't generate prmtop and inpcrd files. what should i do?
>
> the simulation in details is in the attachment.
>
>
>
>
>
> Walston Wang
>
> ------------------------------
>
> Message: 6
> Date: Tue, 24 Mar 2015 22:06:34 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] The unperturbed charge of the unit: -2.980000 is
> not integral
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qwDS3ThZgPsVQoq382UNevS-tdDAMNjaqksHxMsw91iQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Tue, Mar 24, 2015 at 9:40 PM, ?? <whlei.hust.edu.cn> wrote:
>
>> Dear amber users,
>>
>> i generate a protein complex (protein and ligand) by autodock adding
>> polar charges.when i did simulation,it came with a error: "The unperturbed
>> charge of the unit: -2.980000 is not integral". and then i can't generate
>> prmtop and inpcrd files. what should i do?
>>
>
> ?This is a warning. Not an error. It does not prevent tleap from printing
> a prmtop file. Look for an error in your output, and try entering it into
> Google to see if your error has been seen before (it most likely has). If
> previous answers help, you will be able to fix it sooner than waiting for
> us to reply to a question.
>
> ??
>> the simulation in details is in the attachment.
>>
>
> ?There was no attachment.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 24 Mar 2015 23:48:08 -0300
> From: George Tzotzos <gtzotzos.me.com>
> Subject: Re: [AMBER] The unperturbed charge of the unit: -2.980000 is
> not integral
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <D117DD59-DAE0-4FB1-9107-B4088ECD0A2F.me.com>
> Content-Type: text/plain; charset=utf-8
>
> I?ve come across the same issue. If my memory does not fail me, on Jason?s suggestion, I added a fractional charge to one of the atoms of the .mol file to bring the charge to an integer number. In your case whatever fraction is necessary to bring the unit charge to 3.0.
>
> I stand to be corrected if I?m wrong. Jason, my apologies if I misquoted you.
>
> Regards
>
> George
>
>> On 24Mar, 2015, at 10:40 PM, ?? <whlei.hust.edu.cn> wrote:
>>
>> Dear amber users,
>>
>> i generate a protein complex (protein and ligand) by autodock adding polar charges.when i did simulation,it came with a error: "The unperturbed charge of the unit: -2.980000 is not integral". and then i can't generate prmtop and inpcrd files. what should i do?
>>
>> the simulation in details is in the attachment.
>>
>>
>>
>>
>>
>> Walston Wang
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 25 Mar 2015 11:00:26 +0530
> From: Subrata Paul <paul.subrata34.gmail.com>
> Subject: Re: [AMBER] vdw energy and electrostatic energy calculation
> for osmolyte
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CADtCLmjJm9HNM5vJTEztK0o9YWEy+au5wwe05UjV1oRk96A+ww.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> very very thanks Jason
>
> Can I use lie command in cpptraj of amber12 tools ?
>
>
> On Tue, Mar 24, 2015 at 7:25 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Tue, Mar 24, 2015 at 3:31 AM, Subrata Paul <paul.subrata34.gmail.com>
>> wrote:
>>
>>> Dear
>>> Amber User,
>>>
>>> I have simulated a protein-urea-water system in AMBER12. Can we
>> calculate
>>> the vdw energy and electrostatic energy for water and urea around the
>>> protein separately?
>>> any hints ?
>>>
>>
>> ?You can strip out the water using cpptraj and compute the energy of each
>> snapshot (using sander with imin=5). This will represent the urea-urea,
>> protein-protein, and protein-urea interactions. Then strip out the urea
>> and compute the energy of each snapshot?. This will represent the
>> water-water, protein-protein, and protein-water interactions.
>>
>> Alternatively, the "energy" action in cpptraj will let you compute these
>> kinds of interactions, but it is a very simplistic sum-over-pairs energy
>> calculation, so you can't use PME or the dispersion correction (to my
>> knowledge) to correct for cutoff effects.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
>
>
>
>
>
> *With Best RegardsSubrata PaulPhD StudentDept of Chemistry.IIT Guwahati*
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 25 Mar 2015 19:42:16 +0800
> From: Vijay Achari <glycoamber.gmail.com>
> Subject: [AMBER] iterative calculation in CPPTRAJ using "for... do...
> done"
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CA+-itZi=YEVNEbhg7bfpO21zFseo1XPPHWKpV0qNJJ4UQOR=Kw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Sir,
>
>
> I am trying to calculate autocorrelation function.
>
> Normally I use a to run the calculation (shown below: SCRITP(I)). This
> script run in loop. Each time it load the trajectory file using trajin and
> does the calculation.
>
> Instead I would like to load the trajectory only once and do the
> calculation loop-wise as shown in SCRIPT(II). When I tried to run the
> SCRIPT(II), I get error message as below:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *CPPTRAJ: Trajectory Analysis. V14.25 ___ ___ ___ ___ | \/ | \/ |
> \/ | _|_/\_|_/\_|_/\_|_ Reading
> '../../../../only-nc-Format-bcmLyo25perR/bcmLyo25perR.prmtop' as Amber
> TopologyINPUT: Reading Input from STDIN [trajin
> ../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc 15000
> 60000] Reading
> '../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc' as Amber
> NetCDF [unwrap *] UNWRAP: By atom using mask '*' Reference is first
> frame. [for j in {1..128};do]'for': Command not found. 1 errors
> encountered reading input.TIME: Total execution time: 0.0695 seconds.*
>
> Is that possible to run the for command from cpptraj command?
> Or is that any other way to do the calculation by reading the TRAJECTORY
> only once and do the repeated calculation iteratively?
>
>
> Below I have given both the SCRIPT(I) and SCRIPT(II).
>
>
> #####################################################################
> # SCRIPT(I)
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *sys="bcmLyo25perR"path="../../../../only-nc-Format-$sys"top="$sys.prmtop"for
> j in {1..128};docpptraj $path/$top << EOFtrajin
> $path/md-all-bcmLyo25perR.nc 15000 60000unwrap *vector v1 :$j.C11 :$j.C14
> timecorr vec1 v1 out head1-lipid$j-C11_C14.dat order 2 tstep 1 tcorr 25000
> norm drct ptrajformatEOF*
>
> *done*################################################
>
>
> # SCRIPT(II)
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *sys="bcmLyo25perR"path="../../../../only-nc-Format-$sys"top="$sys.prmtop"cpptraj
> $path/$top << EOFtrajin $path/md-all-bcmLyo25perR.nc 15000 60000unwrap *for
> j in {1..128};dovector v1 :$j.C11 :$j.C14 timecorr vec1 v1 out
> head1-lipid$j-C11_C14.dat order 2 tstep 1 tcorr 25000 norm drct
> ptrajformatdoneEOF*
>
> ##############################################
>
>
> Thanks in advance.
> Vijay
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 25 Mar 2015 08:14:00 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] vdw energy and electrostatic energy calculation
> for osmolyte
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qzt2X66gTuWNKuPA640ji1Kpp=jApLXukfT3pKErsdag.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Wed, Mar 25, 2015 at 1:30 AM, Subrata Paul <paul.subrata34.gmail.com>
> wrote:
>
>> very very thanks Jason
>>
>> Can I use lie command in cpptraj of amber12 tools ?
>>
>
> ?If you think that calculates what you want to calculate...
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 11
> Date: Wed, 25 Mar 2015 07:50:26 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] iterative calculation in CPPTRAJ using "for...
> do... done"
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOagBsSXKYFXWjOVXWeycykcatn_ZrDP4-+kpbRqz0gucw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Wed, Mar 25, 2015 at 5:42 AM, Vijay Achari <glycoamber.gmail.com> wrote:
>> Is that possible to run the for command from cpptraj command?
>
> One glance at the manual will show that it is not so.
>
>> Or is that any other way to do the calculation by reading the TRAJECTORY
>> only once and do the repeated calculation iteratively?
>
> Why not use a script to create your input, then run cpptraj? E.g.
>
> cat > input <<EOF
> parm ../../../../only-nc-Format-bcmLyo25perR/bcmLyo25perR.prmtop
> trajin ../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc
> 15000 60000
> EOF
>
> for ((res=1; res < 129; res++)) ; do
> echo "vector v1 :$res.C11 :$res.C14" >> input
> done
>
> cpptraj -i input
>
> -Dan
>
>>
>>
>> Below I have given both the SCRIPT(I) and SCRIPT(II).
>>
>>
>> #####################################################################
>> # SCRIPT(I)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *sys="bcmLyo25perR"path="../../../../only-nc-Format-$sys"top="$sys.prmtop"for
>> j in {1..128};docpptraj $path/$top << EOFtrajin
>> $path/md-all-bcmLyo25perR.nc 15000 60000unwrap *vector v1 :$j.C11 :$j.C14
>> timecorr vec1 v1 out head1-lipid$j-C11_C14.dat order 2 tstep 1 tcorr 25000
>> norm drct ptrajformatEOF*
>>
>> *done*################################################
>>
>>
>> # SCRIPT(II)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *sys="bcmLyo25perR"path="../../../../only-nc-Format-$sys"top="$sys.prmtop"cpptraj
>> $path/$top << EOFtrajin $path/md-all-bcmLyo25perR.nc 15000 60000unwrap *for
>> j in {1..128};dovector v1 :$j.C11 :$j.C14 timecorr vec1 v1 out
>> head1-lipid$j-C11_C14.dat order 2 tstep 1 tcorr 25000 norm drct
>> ptrajformatdoneEOF*
>>
>> ##############################################
>>
>>
>> Thanks in advance.
>> Vijay
>> _______________________________________________
>> 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: Wed, 25 Mar 2015 09:52:06 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] iterative calculation in CPPTRAJ using "for...
> do... done"
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3rba3rhjca7pVAvk8HAFB0w9xcFbpmnz15SrU=M4LQ9QA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Wed, Mar 25, 2015 at 7:42 AM, Vijay Achari <glycoamber.gmail.com> wrote:
>
>> Dear Sir,
>>
>>
>> I am trying to calculate autocorrelation function.
>>
>> Normally I use a to run the calculation (shown below: SCRITP(I)). This
>> script run in loop. Each time it load the trajectory file using trajin and
>> does the calculation.
>>
>> Instead I would like to load the trajectory only once and do the
>> calculation loop-wise as shown in SCRIPT(II). When I tried to run the
>> SCRIPT(II), I get error message as below:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *CPPTRAJ: Trajectory Analysis. V14.25 ___ ___ ___ ___ | \/ | \/ |
>> \/ | _|_/\_|_/\_|_/\_|_ Reading
>> '../../../../only-nc-Format-bcmLyo25perR/bcmLyo25perR.prmtop' as Amber
>> TopologyINPUT: Reading Input from STDIN [trajin
>> ../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc 15000
>> 60000] Reading
>> '../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc' as Amber
>> NetCDF [unwrap *] UNWRAP: By atom using mask '*' Reference is first
>> frame. [for j in {1..128};do]'for': Command not found. 1 errors
>> encountered reading input.TIME: Total execution time: 0.0695 seconds.*
>>
>> Is that possible to run the for command from cpptraj command?
>>
>
> ?No. It is not (currently) supported. Also, I'm not sure how you are
> pasting the output into your email client, but it is coming out mangled,
> making it very hard to decipher and easy to miss important details.
> ?
>
>
>> Or is that any other way to do the calculation by reading the TRAJECTORY
>> only once and do the repeated calculation iteratively?
>>
>
> ?There are two options that I can think of. The first is to use your loops
> in shell scripting to write a cpptraj script, then run that serialized
> script directly. Another way, if you are familiar with Python, is to use
> pytraj (http://github.com/pytraj/pytraj), which will give you access to all
> of cpptraj's functionality combined with the Python interpreter and numpy
> library.
>
> HTH,
> Jason?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 13
> Date: Thu, 26 Mar 2015 00:51:56 +0800
> From: Vijay Achari <glycoamber.gmail.com>
> Subject: Re: [AMBER] iterative calculation in CPPTRAJ using "for...
> do... done"
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CA+-itZhH0oFs0pjD56v=VxoW=EcQRvhJofMdSto3aDrDdhsiAA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thank you Daniel.
>
> Your idea works.
>
> Best wishes.
>
> Vijay
>
> On Wed, Mar 25, 2015 at 9:50 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> On Wed, Mar 25, 2015 at 5:42 AM, Vijay Achari <glycoamber.gmail.com>
>> wrote:
>>> Is that possible to run the for command from cpptraj command?
>>
>> One glance at the manual will show that it is not so.
>>
>>> Or is that any other way to do the calculation by reading the TRAJECTORY
>>> only once and do the repeated calculation iteratively?
>>
>> Why not use a script to create your input, then run cpptraj? E.g.
>>
>> cat > input <<EOF
>> parm ../../../../only-nc-Format-bcmLyo25perR/bcmLyo25perR.prmtop
>> trajin ../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc
>> 15000 60000
>> EOF
>>
>> for ((res=1; res < 129; res++)) ; do
>> echo "vector v1 :$res.C11 :$res.C14" >> input
>> done
>>
>> cpptraj -i input
>>
>> -Dan
>>
>>>
>>>
>>> Below I have given both the SCRIPT(I) and SCRIPT(II).
>>>
>>>
>>> #####################################################################
>>> # SCRIPT(I)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>> *sys="bcmLyo25perR"path="../../../../only-nc-Format-$sys"top="$sys.prmtop"for
>>> j in {1..128};docpptraj $path/$top << EOFtrajin
>>> $path/md-all-bcmLyo25perR.nc 15000 60000unwrap *vector v1 :$j.C11
>> :$j.C14
>>> timecorr vec1 v1 out head1-lipid$j-C11_C14.dat order 2 tstep 1 tcorr
>> 25000
>>> norm drct ptrajformatEOF*
>>>
>>> *done*################################################
>>>
>>>
>>> # SCRIPT(II)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>> *sys="bcmLyo25perR"path="../../../../only-nc-Format-$sys"top="$sys.prmtop"cpptraj
>>> $path/$top << EOFtrajin $path/md-all-bcmLyo25perR.nc 15000 60000unwrap
>> *for
>>> j in {1..128};dovector v1 :$j.C11 :$j.C14 timecorr vec1 v1 out
>>> head1-lipid$j-C11_C14.dat order 2 tstep 1 tcorr 25000 norm drct
>>> ptrajformatdoneEOF*
>>>
>>> ##############################################
>>>
>>>
>>> Thanks in advance.
>>> Vijay
>>> _______________________________________________
>>> 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: 14
> Date: Thu, 26 Mar 2015 00:53:56 +0800
> From: Vijay Achari <glycoamber.gmail.com>
> Subject: Re: [AMBER] iterative calculation in CPPTRAJ using "for...
> do... done"
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CA+-itZh1XR3bCd4WChGhva86829SVnL_VZEzHsEWNWkN4-gPRw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Jason,
>
> I shall try to learn using pytraj in near future.
>
> Thanks for your suggestion anyway.
>
> Regards
> Vijay
>
> On Wed, Mar 25, 2015 at 9:52 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Wed, Mar 25, 2015 at 7:42 AM, Vijay Achari <glycoamber.gmail.com>
>> wrote:
>>
>>> Dear Sir,
>>>
>>>
>>> I am trying to calculate autocorrelation function.
>>>
>>> Normally I use a to run the calculation (shown below: SCRITP(I)). This
>>> script run in loop. Each time it load the trajectory file using trajin
>> and
>>> does the calculation.
>>>
>>> Instead I would like to load the trajectory only once and do the
>>> calculation loop-wise as shown in SCRIPT(II). When I tried to run the
>>> SCRIPT(II), I get error message as below:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *CPPTRAJ: Trajectory Analysis. V14.25 ___ ___ ___ ___ | \/ |
>> \/ |
>>> \/ | _|_/\_|_/\_|_/\_|_ Reading
>>> '../../../../only-nc-Format-bcmLyo25perR/bcmLyo25perR.prmtop' as Amber
>>> TopologyINPUT: Reading Input from STDIN [trajin
>>> ../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc 15000
>>> 60000] Reading
>>> '../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc' as Amber
>>> NetCDF [unwrap *] UNWRAP: By atom using mask '*' Reference is
>> first
>>> frame. [for j in {1..128};do]'for': Command not found. 1 errors
>>> encountered reading input.TIME: Total execution time: 0.0695 seconds.*
>>>
>>> Is that possible to run the for command from cpptraj command?
>>>
>>
>> ?No. It is not (currently) supported. Also, I'm not sure how you are
>> pasting the output into your email client, but it is coming out mangled,
>> making it very hard to decipher and easy to miss important details.
>> ?
>>
>>
>>> Or is that any other way to do the calculation by reading the TRAJECTORY
>>> only once and do the repeated calculation iteratively?
>>>
>>
>> ?There are two options that I can think of. The first is to use your loops
>> in shell scripting to write a cpptraj script, then run that serialized
>> script directly. Another way, if you are familiar with Python, is to use
>> pytraj (http://github.com/pytraj/pytraj), which will give you access to
>> all
>> of cpptraj's functionality combined with the Python interpreter and numpy
>> library.
>>
>> HTH,
>> Jason?
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> ------------------------------
>
> Message: 15
> Date: Wed, 25 Mar 2015 12:30:23 -0500
> From: Brian Radak <brian.radak.accts.gmail.com>
> Subject: [AMBER] trouble running pmemd.cuda
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CANgqt_hUpAxaexN9DXnkdYOXh0Zf3p71Zd8YG9+3sM=8hW-G=A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I've been able to successfully compile pmemd.cuda on a new desktop running
> Ubuntu 14.04 with a Quadro K2200 (I know it probably won't be fast, but it
> has Kepler architecture so it should be good for small tests).
>
>
> This was my sequence:
> configure -cuda gnu
> make -j8
> cd test && make test.cuda
>
> However all of the tests error out and most or all give the msg:
>
> cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
>
> Suggestions?
>
> Possibly relevant - Without thinking I originally installed cuda 7.0. I
> then had to uninstall that as well as the updated driver (346 or
> something?) and then install the "old" 6.5/340 toolkit/driver. I don't
> *think* that was a problem, bc I can compile and run the cuda-samples.
>
> Thanks,
> Brian
>
> --
> Brian Radak
> Postdoctoral Scholar
> University of Chicago
> Department of Biochemistry & Molecular Biology
> Gordon Center for Integrative Science, W323A
> 929 E. 57th St.
> Chicago, IL 60637-1454
> Tel: 773/834-2812
> e-mail: radak.uchicago.edu
>
>
> ------------------------------
>
> Message: 16
> Date: Wed, 25 Mar 2015 10:41:27 -0700
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] trouble running pmemd.cuda
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <0E59295A-7FF7-494D-A2C3-9D9C4062C9D3.rosswalker.co.uk>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Brian,
>
> This sort of thing can occur when the CUDA runtime library that gets used at runtime does not match the CUDA version used to compile the code. This is inline with what you suggest below regarding CUDA 7 etc. I would suggest starting from a brand new Amber untar and build it again. Make sure that your CUDA_HOME variable (and anything in your LD_LIBRARY_PATH) match the cuda compiler version that 'nvcc -V' returns.
>
> If the problem still persists let me know.
>
> All the best
> Ross
>
>> On Mar 25, 2015, at 10:30 AM, Brian Radak <brian.radak.accts.gmail.com> wrote:
>>
>> I've been able to successfully compile pmemd.cuda on a new desktop running
>> Ubuntu 14.04 with a Quadro K2200 (I know it probably won't be fast, but it
>> has Kepler architecture so it should be good for small tests).
>>
>>
>> This was my sequence:
>> configure -cuda gnu
>> make -j8
>> cd test && make test.cuda
>>
>> However all of the tests error out and most or all give the msg:
>>
>> cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
>>
>> Suggestions?
>>
>> Possibly relevant - Without thinking I originally installed cuda 7.0. I
>> then had to uninstall that as well as the updated driver (346 or
>> something?) and then install the "old" 6.5/340 toolkit/driver. I don't
>> *think* that was a problem, bc I can compile and run the cuda-samples.
>>
>> Thanks,
>> Brian
>>
>> --
>> Brian Radak
>> Postdoctoral Scholar
>> University of Chicago
>> Department of Biochemistry & Molecular Biology
>> Gordon Center for Integrative Science, W323A
>> 929 E. 57th St.
>> Chicago, IL 60637-1454
>> Tel: 773/834-2812
>> e-mail: radak.uchicago.edu
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 17
> Date: Wed, 25 Mar 2015 18:55:45 +0100
> From: vladimir.palivec.marge.uochb.cas.cz
> Subject: [AMBER] Free energy calculation: Thermodynamic integration
> with use of restraints
> To: amber.ambermd.org
> Message-ID:
> <d376a9ad382ea16b0bd334a9b3dd61ba.squirrel.marge.uochb.cas.cz>
> Content-Type: text/plain;charset=iso-8859-1
>
>
> Hello,
>
> this question is similar to this one:
>
> http://archive.ambermd.org/201205/0093.html
>
> however, I think I quite did not get it.
>
> I would like to do a thermodynamic integration simulations to calculate dG
> of binding of a ligand to a protein. After search through a literature I
> decided to do it in multiple steps:
>
> 1. constrain a ligand in a certain position using 6 restraints
> - here i need to calculate dG of proposing restraints
>
> 2. turn off el. i.
>
> 3. using soft core, turn off vww interactions
>
> 4. analytically remove restraints
>
>
> I am not sure how to perform the step 1. I thought it is possible to use
> pmemd with single topology and gradually propose restraints and thus get
> the dG (with use of nmropt=1 and DIANG file). However, I have no found any
> way to do it - either in manual or forum. Please, can somebody give me a
> hint how this calculation should be performed? How to set up the
> calculation and how to obtain energy of proposing restraints?
>
> Is it even possible to do it with one topology file?
>
> Thank you very much for any help!
>
> Vlada
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 18
> Date: Thu, 26 Mar 2015 00:10:58 +0530
> From: Subrata Paul <paul.subrata34.gmail.com>
> Subject: Re: [AMBER] vdw energy and electrostatic energy calculation
> for osmolyte
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CADtCLmgQ=Bcc5oWF=KN9gAbiZjekdfh6tj9FZ=D7-15N=E8GLA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Jason
>
> I want to calculate vdw energy and electrostatic energy for the first
> solvation shell.
> Do lie command calculate the energy for FSS in amber 12 tools ?
>
> On Wed, Mar 25, 2015 at 5:44 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Wed, Mar 25, 2015 at 1:30 AM, Subrata Paul <paul.subrata34.gmail.com>
>> wrote:
>>
>>> very very thanks Jason
>>>
>>> Can I use lie command in cpptraj of amber12 tools ?
>>>
>>
>> ?If you think that calculates what you want to calculate...
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
>
>
>
>
>
> *With Best RegardsSubrata PaulPhD StudentDept of Chemistry.IIT Guwahati*
>
>
> ------------------------------
>
> Message: 19
> Date: Wed, 25 Mar 2015 13:46:24 -0500
> From: Brian Radak <brian.radak.accts.gmail.com>
> Subject: Re: [AMBER] trouble running pmemd.cuda
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CANgqt_hmKVaswJj-m5KaLmHWwDT2wrB8FGvoyeAZzHK6g3kS7w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Ah yes, the compiling equivalent of "turning it off and on again."
> Unfortunately it looks like the result is the same.
>
> Double checking my CUDA_HOME, etc. settings:
>
>>> nvcc -V
> nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2014 NVIDIA Corporation
> Built on Thu_Jul_17_21:41:27_CDT_2014
> Cuda compilation tools, release 6.5, V6.5.12
>>> echo $CUDA_HOME
> /usr/local/cuda-6.5
>>> echo $LD_LIBRARY_PATH
> /home/radak/software/amber14/lib:/usr/local/cuda-6.5/lib64:/usr/local/cuda-6.5/lib
>
> The CUDA install instructions I found suggested the "lib64" addition above,
> but the AMBER install msg only suggests "lib". Is that all cool?
>
>
>
> On Wed, Mar 25, 2015 at 12:41 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Brian,
>>
>> This sort of thing can occur when the CUDA runtime library that gets used
>> at runtime does not match the CUDA version used to compile the code. This
>> is inline with what you suggest below regarding CUDA 7 etc. I would suggest
>> starting from a brand new Amber untar and build it again. Make sure that
>> your CUDA_HOME variable (and anything in your LD_LIBRARY_PATH) match the
>> cuda compiler version that 'nvcc -V' returns.
>>
>> If the problem still persists let me know.
>>
>> All the best
>> Ross
>>
>>> On Mar 25, 2015, at 10:30 AM, Brian Radak <brian.radak.accts.gmail.com>
>> wrote:
>>>
>>> I've been able to successfully compile pmemd.cuda on a new desktop
>> running
>>> Ubuntu 14.04 with a Quadro K2200 (I know it probably won't be fast, but
>> it
>>> has Kepler architecture so it should be good for small tests).
>>>
>>>
>>> This was my sequence:
>>> configure -cuda gnu
>>> make -j8
>>> cd test && make test.cuda
>>>
>>> However all of the tests error out and most or all give the msg:
>>>
>>> cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
>>>
>>> Suggestions?
>>>
>>> Possibly relevant - Without thinking I originally installed cuda 7.0. I
>>> then had to uninstall that as well as the updated driver (346 or
>>> something?) and then install the "old" 6.5/340 toolkit/driver. I don't
>>> *think* that was a problem, bc I can compile and run the cuda-samples.
>>>
>>> Thanks,
>>> Brian
>>>
>>> --
>>> Brian Radak
>>> Postdoctoral Scholar
>>> University of Chicago
>>> Department of Biochemistry & Molecular Biology
>>> Gordon Center for Integrative Science, W323A
>>> 929 E. 57th St.
>>> Chicago, IL 60637-1454
>>> Tel: 773/834-2812
>>> e-mail: radak.uchicago.edu
>>> _______________________________________________
>>> 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
>>
>
>
>
> --
> Brian Radak
> Postdoctoral Scholar
> University of Chicago
> Department of Biochemistry & Molecular Biology
> Gordon Center for Integrative Science, W323A
> 929 E. 57th St.
> Chicago, IL 60637-1454
> Tel: 773/834-2812
> e-mail: radak.uchicago.edu
>
>
> ------------------------------
>
> Message: 20
> Date: Wed, 25 Mar 2015 14:47:02 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] vdw energy and electrostatic energy calculation
> for osmolyte
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <7204E71D-F2F0-456D-AFE4-9F62DA1CB8F8.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
>
>> On Mar 25, 2015, at 2:40 PM, Subrata Paul <paul.subrata34.gmail.com> wrote:
>>
>> Dear Jason
>>
>> I want to calculate vdw energy and electrostatic energy for the first
>> solvation shell.
>> Do lie command calculate the energy for FSS in amber 12 tools ?
>
> Not easily. You will probably need to use the ?closest? command in cpptraj to create a system that only has the first solvation shell, create a corresponding prmtop file for that new trajectory, then use the ?lie? or ?energy? commands on the resulting trajectory.
>
> Alternatively you can simply use a very small cutoff, but the energies will be very noisy on account of the cutoff being a truly horrible approach to long-range electrostatics.
>
> Note that ?first solvation shell? is not really rigorously defined to my knowledge (although everybody ?knows? what it is). So you need to use some algorithmic definition for selecting the atoms in the first solvation shell and go with that. Also note that energy is an extensive property, so if different frames have different numbers of waters *in* that first solvation shell, their energies will not be directly comparable (which is why the ?closest? command is probably a better approach than the hard cutoff).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
> ------------------------------
>
> Message: 21
> Date: Wed, 25 Mar 2015 14:49:52 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] trouble running pmemd.cuda
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <997920F8-DB15-4A39-A6AE-D6BD050AA509.gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
>
>> On Mar 25, 2015, at 2:46 PM, Brian Radak <brian.radak.accts.gmail.com> wrote:
>>
>> Ah yes, the compiling equivalent of "turning it off and on again."
>> Unfortunately it looks like the result is the same.
>>
>> Double checking my CUDA_HOME, etc. settings:
>>
>>>> nvcc -V
>> nvcc: NVIDIA (R) Cuda compiler driver
>> Copyright (c) 2005-2014 NVIDIA Corporation
>> Built on Thu_Jul_17_21:41:27_CDT_2014
>> Cuda compilation tools, release 6.5, V6.5.12
>>>> echo $CUDA_HOME
>> /usr/local/cuda-6.5
>>>> echo $LD_LIBRARY_PATH
>> /home/radak/software/amber14/lib:/usr/local/cuda-6.5/lib64:/usr/local/cuda-6.5/lib
>>
>> The CUDA install instructions I found suggested the "lib64" addition above,
>> but the AMBER install msg only suggests "lib". Is that all cool?
>
> Both is probably better (my LD_LIBRARY_PATH is ...:/opt/cuda/6.5/lib:/opt/cuda/6.5/lib64:...). $CUDA_HOME/lib on my machine only contains the runtime libraries -- all of the other libraries (like libcufft and libcublas) are in lib64, and at least cufft is needed for pmemd.cuda...
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1169, Issue 1
> **************************************


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Received on Wed Mar 25 2015 - 15:00:03 PDT
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