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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
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AMBER Mailing List Digest
Today's Topics:
1. Re: Diffusion constant calculation (pooja chahal)
2. Error with quasi-harmonic MMPBSA.py calculations (Abhishek TYAGI)
3. Re: Evaluating hydrogen boding lifetime (Vijay Achari)
4. Alanin scanning MMGBSA.py error: TypeError: not all arguments
converted during string formatting (maryam azimzadehirani)
5. Re: Alanin scanning MMGBSA.py error: TypeError: not all
arguments converted during string formatting (Jason Swails)
6. Re: Error with quasi-harmonic MMPBSA.py calculations
(Jason Swails)
7. Writing out restart files (gepaula.web.de)
8. Re: Writing out restart files (Christina Bergonzo)
9. Re: Writing out restart files (Daniel Roe)
10. Re: Evaluating hydrogen boding lifetime (Daniel Roe)
11. Re: Writing out restart files (Jason Swails)
12. Re: Diffusion constant calculation (Daniel Roe)
13. all in one pc for MD simulation calculations (Atila Petrosian)
14. Re: all in one pc for MD simulation calculations (Jason Swails)
15. NMode Analysis Using Truncated Trajectory (Laura Tociu)
----------------------------------------------------------------------
Message: 1
Date: Thu, 16 Apr 2015 09:12:21 +0530
From: pooja chahal <chahal.pooja.rs.gmail.com>
Subject: Re: [AMBER] Diffusion constant calculation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAHO-wZ_ucyt03vwMC0GyjXcZdwidqQM_NLxbJR=r82F=Ev4RfQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
I am using cpptraj (AMBER 12 version ). The input file for cpptraj that I
am using is as follow:
trajin traj1
trajin traj2
unwrap
trajout x.out pdb multi nobox
I am getting following error:
ACTIONS: Initializing 1 actions:
0: [unwrap]
PTRAJ ACTION: [unwrap]
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [abc.parm7]: Setting up 1 actions.
0: [unwrap]
Mask [*] represents 23012 atoms
UNWRAP
The atoms in the calculation follow: * (All atoms are selected)
----- [abc_prod1.mdcrd] (1-1000, 1) -----
0% Warning: Action [unwrap] failed, frame 0.
On Wed, Apr 15, 2015 at 10:43 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Apr 15, 2015 at 6:25 AM, pooja chahal <chahal.pooja.rs.gmail.com>
> wrote:
> > Thanks for the reply. I have tried cpptraj following your suggestion but
> I
> > am unable to unwrap the trajectory using cpptraj. I have no prior
> > experience of using cpptraj. Also asterisks are not observed in the
> > original ASCII trajectory file. As I have mentioned earlier, I have used
> > iwrap=1 during my production run.
>
> Could you provide some more detail on how you were unable to unwrap
> with cpptraj? Does it not recognize the command? Does it give an error
> message? What version of cpptraj have you tried?
>
> -Dan
>
> >
> > On Tue, Apr 14, 2015 at 7:36 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> On Mon, Apr 13, 2015 at 10:42 PM, pooja chahal
> >> <chahal.pooja.rs.gmail.com> wrote:
> >> > Also one more thing that I am observing is that while generating .pdb
> >> files
> >> > using ptraj with unwrap command, some of atoms attains a very high
> >> negative
> >> > value (< -1000) for coordinates. For these coordinates "********"
> appears
> >> > in the .pdb file instead of real coordinates. However, this is not the
> >> only
> >>
> >> This seems odd to me. The multiple asterisks is something that fortran
> >> code does for numerical overflow, not C/C++ code (to my knowledge).
> >> You shouldn't be getting asterisks in your PDB files if you're
> >> creating them with ptraj. Do you get the same behavior with cpptraj?
> >>
> >> If on the other hand you mean you see asterisks in the original ASCII
> >> trajectory file then your coordinates overflowed during your
> >> simulation and there is no way to recover them. For this reason it is
> >> recommended that during simulations you use 'iwrap=1' to enable
> >> imaging, 'ioutfm=1' to write NetCDF trajectories, and 'ntxo=2' to
> >> write NetCDF restart files; the NetCDF file format is not nearly as
> >> susceptible to issues as the ASCII format.
> >>
> >> Hope this helps,
> >>
> >> -Dan
> >>
> >> --
> >> -------------------------
> >> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 2
Date: Thu, 16 Apr 2015 04:26:20 +0000
From: Abhishek TYAGI <atyagiaa.connect.ust.hk>
Subject: [AMBER] Error with quasi-harmonic MMPBSA.py calculations
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID: <1429158383752.93166.connect.ust.hk>
Content-Type: text/plain; charset="iso-8859-1"
Dear Experts,
Installed MMPBSA.py.MPI on gpu cluster successfully, have following questions:
1. Running on serial MMPBSA.py I am able to run the mmpbsa.in file with all the desired result.
2. I am able to perform GB and Decomposition calculations without any problem using
mpirun -np 60 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o Final_rresult.dat -do Final_decom.dat -sp solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y last5ns.dcd > out.log
2. When I run entropy calculations, the problem appears as in form of error "Error with quasi-harmonic MMPBSA.py calculations"
input file:
Input file for running PB and GB
&general
startframe=1, endframe=200, verbose=2, keep_files=2, strip_mask=":WAT:SOD:CLA", interval=1, entropy=1,
/
&gb
igb=1, saltcon=0.100,
/
&decomp
idecomp=1,
dec_verbose=1,
/
I will be very thankful for the reply.
Thanks in advance
Regards
Abhi
------------------------------
Message: 3
Date: Thu, 16 Apr 2015 14:41:54 +0800
From: Vijay Achari <glycoamber.gmail.com>
Subject: Re: [AMBER] Evaluating hydrogen boding lifetime
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CA+-itZg+xzo2UOd8DtwT-s1mHCRpQM5kdQvUy6WaRAtLcq3hsg.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear Sir,
Relating to hydrogen bonding calculations, now I would like to calculate
the values for *water bridging*.
Could you kindly brief me on how to calculate the number of bridging water
from the HB calculation that I already done as indicated earlier mail in
this post?
Thanks
Vijay
On Tue, Mar 24, 2015 at 11:42 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> Dear Daniel,
>
> If you dont mind, could you provide the citation relevent for the
> implementation of HB lifetime calcultion?
>
> Thanks in advance.
>
> Vijay
>
> On Sun, Mar 22, 2015 at 1:23 PM, Vijay Achari <glycoamber.gmail.com>
> wrote:
>
>> Dear Daniel,
>>
>> I was away and now I am back.
>>
>> Thanks for your reply.
>>
>> Since I am working on disaccharide glycolipids, I have 11 acceptors
>> (O11,O12,O13,O14,O15,O16,O22,O23,O24,O25,O26), and 7 hydroxyl groups
>> (O12-H12, O13-H13, O16-H16, O22-H22, O23-H23, O24-H24, O26-H26).
>>
>> My main target was to know, in average, how long each acceptor (O) of a
>> glycolipid involve in hydrogen bonding interaction no matter which donor is
>> involved, in the glycolipid bilayer assembly.
>>
>> So to achieve this, I selected columns only with "O22" (for example:
>> BMR_42.O22-BMR, BMR_49.O22-BMR, BMR_59.O22-BMR, BMR_23.O22-BMR,
>> BMR_10.O22-BMR BMR_61.O22-BMR) and sum up all the "1s" and divided with
>> the total number of frames involved. I repeated this procedure for each
>> acceptors.
>>
>> If I am not mistaken, I guess what you have suggested is what I want
>> actually. But I did not use *readdata* and *lifeltime* commands to get
>> the final value. I used an awk script to do the selections column wise and
>> average over all frames.
>>
>> Welcome any feedback from your side to enhance my understanding.
>>
>> Thank you.
>> Vijay
>>
>>
>>
>>
>> On Sun, Mar 22, 2015 at 12:06 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> You still haven't said whether I was right or wrong about you wanting
>>> to calculate the lifetime of a certain solute atom (or residue) being
>>> involved in *any* hydrogen bond. Since you haven't said no, I will
>>> proceed on the assumption that this is what you want. In that case
>>> this is the procedure I would use.
>>>
>>> 1) Calculate the hydrogen bond time series data (you have done this).
>>>
>>> 2) Use a script to sum up all columns involving your atom/residue of
>>> interest. This could be as simple as visually identifying which
>>> columns contain the data you need (e.g. columns 2, 4, 5, and 7) and
>>> using something like awk:
>>>
>>> awk '{print $2 + $4 + $5 + $7}' solutehb.dat > sum.dat
>>>
>>> 3) Read the summed data back into cpptraj with readdata:
>>>
>>> readdata sum.dat
>>>
>>> 4) Perform lifetime analysis on the summed data. The default settings
>>> for cutoff etc will still work since anything greater than 0 means a
>>> hydrogen bond is present:
>>>
>>> lifetime sum.dat out life.sum.dat ...
>>>
>>> -Dan
>>>
>>> On Mon, Mar 16, 2015 at 10:50 AM, Vijay Achari <glycoamber.gmail.com>
>>> wrote:
>>> > Dear Dan,
>>> >
>>> > Below is the example you gave to explain on how the calculation of HB
>>> can
>>> > done with raw data.
>>> >
>>> >
>>> > HB1-1 HB1-2
>>> > 1 0
>>> > 0 1
>>> > 1 0
>>> > 1 1
>>> >
>>> > Using the method I illustrated before you'd come up with an average of
>>> > (5 / 4 = 1.25). However, the actual answer of how often is HB1
>>> > involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
>>> > is broken, HB1-2 is formed, so its always involved in some kind of
>>> > hydrogen bond. So to do what you want you will need to write out the
>>> > raw time series data, sum up the columns corresponding to the hydrogen
>>> > bonds you are interested in, then run 'lifetime' analysis on that data
>>> > set. So using the above sets as an example, the set I would actually
>>> > run lifetime analysis on would look like:
>>> >
>>> >
>>> > Relating to the above example, I understand that we need to add the
>>> "1"s
>>> > and divide by total number of lines.
>>> >
>>> > (total of all "1"s) / (total rows with "1"s)
>>> >
>>> >
>>> > So how with the example below? (I modified the above sample).
>>> >
>>> > HB1-1 HB1-2
>>> > 1 0
>>> > 0 1
>>> > 1 0
>>> > 1 1
>>> > 0 1
>>> > 0 0
>>> > 0 0
>>> >
>>> > For the above example is the the average is 6/7 or 6/5. The number 7
>>> > stand for total number of rows and the later stand for rows with the
>>> > presence of "1" (at least once).
>>> >
>>> > Means do I need to count the total rows or the rows with the
>>> occurrence of
>>> > "1" only?
>>> >
>>> >
>>> >
>>> > Your explanation would help me to write the script.
>>> >
>>> > Thanks.
>>> >
>>> >
>>> >
>>> > On Thu, Mar 12, 2015 at 4:53 PM, Vijay Achari <glycoamber.gmail.com>
>>> wrote:
>>> >
>>> >> Dear Dan,
>>> >>
>>> >> Following your explanation, I would like to verify few things.
>>> >>
>>> >> #1) The file that contains the raw data; is this one "solutehb.dat"
>>> >>
>>> >> if yes,
>>> >>
>>> >> #2) The format of the data in the file is as below?
>>> >>
>>> >> #Frame *BMR_42.O22-BMR_1.O23-H23* BMR_49.O13-BMR_1.O13-H13
>>> >> BMR_59.O13-BMR_2.O22-H22 BMR_10.O13-BMR_2.O26-H26 BMR_61.O26-BMR_3
>>> .O22-H22
>>> >> BMR_23.
>>> >> O25-BMR_4.O12-H12 BMR_23.O26-BMR_4.O13-H13 BMR_23.O25-BMR_4.O13-H13
>>> >> BMR_20.O13-BMR_5.O22-H22 BMR_10.O24-BMR_6.O13-H13 BMR_41.O23-BMR_7
>>> .O23-H2
>>> >> 3 BMR_41.O24-BMR_7.O23-H23 ....
>>> >>
>>> >>
>>> >> * 1 * 1
>>> >> 1 1 1
>>> >> 1 1 1
>>> >> 1 1 1
>>> >> 1 1 1
>>> >> 1 1 1
>>> >> 1 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1
>>> >> 1 1 1 . . .
>>> >>
>>> >>
>>> >> #3) So need I operate on this file?
>>> >>
>>> >> #4) Is the first data "BMR_42.O22-BMR_1.O23-H23" is corresponding to
>>> the
>>> >> value "1" (below #2)
>>> >>
>>> >> Thank you.
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> On Wed, Mar 11, 2015 at 11:11 PM, Daniel Roe <daniel.r.roe.gmail.com>
>>> >> wrote:
>>> >>
>>> >>> Hi,
>>> >>>
>>> >>> Sorry, it's not clear to me what you're trying to calculate. You said
>>> >>> "I want to know the lifetime of HB for O22 (ACCEPTOR) atom only"; do
>>> >>> you want the average lifetime of any given O22 involved in a hydrogen
>>> >>> bond? In that case you will probably need to write your own script
>>> for
>>> >>> it for the time being. I'll try to illustrate why with an example.
>>> Say
>>> >>> I want to ask how often is BMR_49.O22 involved in any hydrogen bond
>>> as
>>> >>> an acceptor. I could naively sum up the total number of frames the
>>> >>> bond is present (TotFrames) for each instance of this acceptor atom
>>> >>> and then divide by the total number of lifetimes:
>>> >>>
>>> >>> 4 20 5 1.8500 37
>>> >>> BMR_49.O22-BMR_1.O26-H26
>>> >>> 7 28 2 1.0357 29
>>> >>> BMR_49.O22-BMR_1.O13-H13
>>> >>>
>>> >>> the total number frames there is a hydrogen bond is 66, and the total
>>> >>> number of lifetimes is 48, so the average lifetime for BMR_49.O22
>>> >>> involved in any hydrogen bond (given the data here) is 1.375 frames.
>>> >>> However, this is only true if the data were sequential, because it
>>> >>> doesn't take into account the times when one is present and the other
>>> >>> isn't. For example, given this hydrogen bond data (where HB1
>>> >>> represents a single acceptor):
>>> >>>
>>> >>> HB1-1 HB1-2
>>> >>> 1 0
>>> >>> 0 1
>>> >>> 1 0
>>> >>> 1 1
>>> >>>
>>> >>> Using the method I illustrated before you'd come up with an average
>>> of
>>> >>> (5 / 4 = 1.25). However, the actual answer of how often is HB1
>>> >>> involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
>>> >>> is broken, HB1-2 is formed, so its always involved in some kind of
>>> >>> hydrogen bond. So to do what you want you will need to write out the
>>> >>> raw time series data, sum up the columns corresponding to the
>>> hydrogen
>>> >>> bonds you are interested in, then run 'lifetime' analysis on that
>>> data
>>> >>> set. So using the above sets as an example, the set I would actually
>>> >>> run lifetime analysis on would look like:
>>> >>>
>>> >>> (HB1-1)+(HB1-2)
>>> >>> 1
>>> >>> 1
>>> >>> 1
>>> >>> 2
>>> >>>
>>> >>> Hope this helps,
>>> >>>
>>> >>> -Dan
>>> >>>
>>> >>> On Wed, Mar 11, 2015 at 12:57 AM, Vijay Achari <glycoamber.gmail.com
>>> >
>>> >>> wrote:
>>> >>> > Dear Dan,
>>> >>> >
>>> >>> > In my case the time gap in between two frames (taken for analysis)
>>> is
>>> >>> 5ps.
>>> >>> >
>>> >>> > #Set Nlifetimes MaxLT AvgLT TotFrames SetName
>>> >>> > 0 17 215 55.7059 947
>>> >>> > BMR_42.O22-BMR_1.O23-H23
>>> >>> > 1 1 1 1.0000 1
>>> >>> > BMR_42.O23-BMR_1.O23-H23
>>> >>> > 2 31 3 1.0968 34
>>> >>> > BMR_31.O22-BMR_1.O26-H26
>>> >>> > 3 11 2 1.0909 12
>>> >>> > BMR_31.O13-BMR_1.O26-H26
>>> >>> > 4 20 5 1.8500 37
>>> >>> > BMR_49.O22-BMR_1.O26-H26
>>> >>> > 5 24 4 1.7917 43
>>> >>> > BMR_49.O23-BMR_1.O26-H26
>>> >>> > 6 41 2 1.0488 43
>>> >>> > BMR_49.O12-BMR_1.O12-H12
>>> >>> > 7 28 2 1.0357 29
>>> >>> > BMR_49.O22-BMR_1.O13-H13
>>> >>> > 8 1 1000 1000.0000 1000
>>> >>> > BMR_49.O13-BMR_1.O13-H13
>>> >>> > 9 1 1 1.0000 1
>>> >>> > BMR_22.O12-BMR_2.O22-H22
>>> >>> > 10 50 62 18.9400 947
>>> >>> > BMR_59.O13-BMR_2.O22-H22
>>> >>> > 11 1 1 1.0000 1
>>> >>> > BMR_59.O25-BMR_2.O23-H23
>>> >>> > 12 34 5 1.1471 39
>>> >>> > BMR_59.O13-BMR_2.O23-H23
>>> >>> > 13 7 6 2.1429 15
>>> >>> > BMR_59.O26-BMR_2.O24-H24
>>> >>> > 14 6 8 3.6667 22
>>> >>> > BMR_59.O25-BMR_2.O24-H24
>>> >>> > 15 28 2 1.1071 31
>>> >>> > BMR_10.O26-BMR_2.O26-H26
>>> >>> > 16 52 121 15.1346 787
>>> >>> > BMR_10.O25-BMR_2.O26-H26
>>> >>> > 17 65 9 1.9231 125
>>> >>> > BMR_10.O13-BMR_2.O26-H26
>>> >>> > 18 4 4 2.2500 9
>>> >>> > BMR_59.O26-BMR_2.O26-H26
>>> >>> > 19 9 1 1.0000 9
>>> >>> > BMR_22.O15-BMR_2.O13-H13
>>> >>> > 20 1 1 1.0000 1
>>> >>> > BMR_10.O11-BMR_2.O16-H16
>>> >>> > 21 7 2 1.1429 8
>>> >>> > BMR_53.O13-BMR_2.O16-H16
>>> >>> > 22 2 3 2.5000 5
>>> >>> > BMR_33.O13-BMR_3.O22-H22
>>> >>> > 23 97 54 6.8247 662
>>> >>> > BMR_61.O26-BMR_3.O22-H22
>>> >>> > 24 1 1 1.0000 1
>>> >>> > BMR_29.O26-BMR_3.O23-H23
>>> >>> > 25 31 36 3.3226 103
>>> >>> > BMR_29.O16-BMR_3.O23-H23
>>> >>> > 26 22 2 1.2273 27
>>> >>> > BMR_30.O22-BMR_3.O23-H23
>>> >>> > 27 4 1 1.0000 4
>>> >>> > BMR_33.O22-BMR_3.O23-H23
>>> >>> > 28 38 2 1.1316 43
>>> >>> > BMR_33.O13-BMR_3.O23-H23
>>> >>> > (there are more than 2000 lines, but I work on only 28 lines to
>>> get some
>>> >>> > understanding)
>>> >>> >
>>> >>> >
>>> >>> > For clarity, I shall show you how I worked on the given results
>>> above.
>>> >>> >
>>> >>> > I want to know the lifetime of HB for O22 (ACCEPTOR) atom only.
>>> So, I
>>> >>> did
>>> >>> > in this way,
>>> >>> >
>>> >>> > 1) sum the values from column AvgLT for the only occurrences of
>>> O22.
>>> >>> > 2) than find the average of that, where the denominator would be
>>> the
>>> >>> number
>>> >>> > of occurrences of O22.
>>> >>> >
>>> >>> > Based on the above steps, the results are :
>>> >>> >
>>> >>> > O22 occur 6 times,
>>> >>> > sum of O22 is 61.916, and
>>> >>> > average of O22 is 10.319.
>>> >>> >
>>> >>> > So, I figured out the lifetime of O22 would be 10.319 x 5ps =
>>> 51.595
>>> >>> ps.
>>> >>> >
>>> >>> > Is this correct? Did I choose the correct column "AvgLT"?
>>> >>> >
>>> >>> > I hope to get some feedback if this is correct way to do it.
>>> >>> >
>>> >>> > Many thanks in advance.
>>> >>> >
>>> >>> > Vijay
>>> >>> >
>>> >>> >
>>> >>> > On Wed, Mar 11, 2015 at 11:50 AM, Daniel Roe <
>>> daniel.r.roe.gmail.com>
>>> >>> wrote:
>>> >>> >
>>> >>> >> On Tue, Mar 10, 2015 at 9:24 PM, Vijay Achari <
>>> glycoamber.gmail.com>
>>> >>> >> wrote:
>>> >>> >> > Could you explain on how to get the lifetime value in pico
>>> second
>>> >>> (ps)?
>>> >>> >>
>>> >>> >> This depends on how often you recorded your coordinate
>>> trajectory. For
>>> >>> >> example, say you ran a simulation with a timestep of 2 fs
>>> (dt=0.002
>>> >>> >> ps) and you recorded a trajectory frame every 500 steps
>>> (ntwx=500).
>>> >>> >> This means that each frame in your trajectory has been recorded
>>> at 1
>>> >>> >> ps intervals. However, say you recorded your trajectory every 5000
>>> >>> >> steps instead - your trajectory then will have been recorded at
>>> 10 ps
>>> >>> >> intervals. Since lifetimes are always given in frames, it should
>>> be
>>> >>> >> easy to convert to ps based on how often your coordinate
>>> trajectory
>>> >>> >> was written to (e.g. in the latter case a max lifetime of 1 frame
>>> >>> >> would mean 10 ps).
>>> >>> >>
>>> >>> >> Hope this helps,
>>> >>> >>
>>> >>> >> -Dan
>>> >>> >>
>>> >>> >> >
>>> >>> >> > Thanks in advance.
>>> >>> >> > Vijay
>>> >>> >> >
>>> >>> >> >
>>> >>> >> > On Tue, Mar 10, 2015 at 10:15 PM, Daniel Roe <
>>> daniel.r.roe.gmail.com
>>> >>> >
>>> >>> >> wrote:
>>> >>> >> >
>>> >>> >> >> Hi,
>>> >>> >> >>
>>> >>> >> >> On Tue, Mar 10, 2015 at 2:53 AM, Vijay Achari <
>>> glycoamber.gmail.com
>>> >>> >
>>> >>> >> >> wrote:
>>> >>> >> >> > generate two files with lifetime information. The
>>> >>> >> *solute.lifetime.dat*
>>> >>> >> >> contain
>>> >>> >> >> > info like:
>>> >>> >> >> >
>>> >>> >> >> > #Set Nlifetimes MaxLT AvgLT TotFrames
>>> SetName
>>> >>> >> >> > 0 22 1 1.0000
>>> 22
>>> >>> >> >> BMR_3.O16-BMR_1.O22-H22
>>> >>> >> >> > 1 296 346 15.6959 4646
>>> >>> >> >> BMR_42.O22-BMR_1.O22-H22
>>> >>> >> >> > 2 992 12 1.4688
>>> 1457
>>> >>> >> >> BMR_42.O14-BMR_1.O22-H22
>>> >>> >> >> > 3 1 1 1.0000
>>> 1
>>> >>> >> >> BMR_42.O13-BMR_1.O22-H22
>>> >>> >> >> > 4 189 12 1.1429
>>> 216
>>> >>> >> >> BMR_57.O25-BMR_1.O22-H22
>>> >>> >> >> > 5 462 410 12.3074 5686
>>> >>> >> >> BMR_57.O16-BMR_1.O22-H22
>>> >>> >> >> >
>>> >>> >> >> > I would like to know how I can go from here to calculate the
>>> >>> >> hb-lifetime
>>> >>> >> >> between
>>> >>> >> >> > solute and solute?
>>> >>> >> >>
>>> >>> >> >> I'm not really sure I understand your question. The data
>>> output you
>>> >>> >> >> posted is exactly the lifetime calculation. For example, the
>>> second
>>> >>> >> >> set (1) contains lifetime information for the hydrogen bond
>>> between
>>> >>> >> >> residue 42, atom O22 and residue 1, atoms O22-H22; there were
>>> 296
>>> >>> >> >> individual lifetimes (i.e. the hbond formed 296 times), the
>>> max of
>>> >>> >> >> which lasted 346 frames, the average lifetime is ~15.7 frames.
>>> Let
>>> >>> me
>>> >>> >> >> know if I'm not understanding you or if I can explain more.
>>> >>> >> >>
>>> >>> >> >> -Dan
>>> >>> >> >>
>>> >>> >> >> >
>>> >>> >> >> > I have read the pages 556-557 from AMBER 14 manual, but I
>>> find it
>>> >>> >> >> difficult
>>> >>> >> >> > to see how one should start processing and getting the
>>> lifetime
>>> >>> value.
>>> >>> >> >> >
>>> >>> >> >> > I think simple example would help me much in this case.
>>> >>> >> >> >
>>> >>> >> >> > Could you give me some example on how this can be obtained?
>>> >>> >> >> >
>>> >>> >> >> > Your help is much appreciated.
>>> >>> >> >> >
>>> >>> >> >> > Thank you.
>>> >>> >> >> > 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
>>> >>> >> >>
>>> >>> >> > _______________________________________________
>>> >>> >> > 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)
>>> >>>
>>> >>> _______________________________________________
>>> >>> 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: Thu, 16 Apr 2015 15:06:05 +0800
From: maryam azimzadehirani <maryamai1988.gmail.com>
Subject: [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all
arguments converted during string formatting
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEVOLfpkZ4Ab-vKfAiMEj7meroZ+1tsmio1aRtYtL0p9=i19jQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear amber users,
I am trying to run alanine scanning with MMGBSA.py. I generated all the
complex,ligand,receptor and mutated files together but I get this error
after running the job:
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using
/usr/local/packages/amber12/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/packages/amber12/amber12/bin/cpptraj
Preparing trajectories for simulation...
Mutating trajectories...
*TypeError: not all arguments converted during string formatting*
Exiting. All files have been retained.
I have looked the mailing list for the similar bugs. Found this one which
seems like a similar case to mine
http://archive.ambermd.org/201409/0035.html since I also mutated a residue
in the ligand. Just couldn?t get the final solution for the error...
will be grateful if you advise,
Maryam
------------------------------
Message: 5
Date: Thu, 16 Apr 2015 09:33:00 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Alanin scanning MMGBSA.py error: TypeError: not
all arguments converted during string formatting
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3r7c9M3F957=pwVFQeGrDF=Pv1czMTRgpG6fqujo9s63Q.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
What version of Amber are you running?
Can you set debug_printlevel=2 in the &general section of your input file
and try running again?
I suspect that the error you are seeing is a mistake I made in creating an
error message that outlines the *real* problem.
Thanks,
Jason
On Thu, Apr 16, 2015 at 3:06 AM, maryam azimzadehirani <
maryamai1988.gmail.com> wrote:
> Dear amber users,
> I am trying to run alanine scanning with MMGBSA.py. I generated all the
> complex,ligand,receptor and mutated files together but I get this error
> after running the job:
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /usr/local/packages/amber12/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /usr/local/packages/amber12/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> Mutating trajectories...
> *TypeError: not all arguments converted during string formatting*
> Exiting. All files have been retained.
>
> I have looked the mailing list for the similar bugs. Found this one which
> seems like a similar case to mine
> http://archive.ambermd.org/201409/0035.html since I also mutated a
> residue
> in the ligand. Just couldn?t get the final solution for the error...
> will be grateful if you advise,
> Maryam
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 6
Date: Thu, 16 Apr 2015 09:40:26 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3q-ZpxcT0XYFtFZYZ3J4rn_ytk7FHS-5ns5uhUMpiP4CA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On Thu, Apr 16, 2015 at 12:26 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk>
wrote:
> Dear Experts,
>
>
> Installed MMPBSA.py.MPI on gpu cluster successfully, have following
> questions:
>
>
> 1. Running on serial MMPBSA.py I am able to run the mmpbsa.in file with
> all the desired result.
>
> 2. I am able to perform GB and Decomposition calculations without any
> problem using
>
>
> mpirun -np 60 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o
> Final_rresult.dat -do Final_decom.dat -sp solvated.prmtop -cp
> complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y last5ns.dcd >
> out.log
>
>
> 2. When I run entropy calculations, the problem appears as in form of
> error "Error with quasi-harmonic MMPBSA.py calculations"
>
>
> input file:
>
> Input file for running PB and GB
>
> &general
>
>
> startframe=1, endframe=200, verbose=2, keep_files=2,
> strip_mask=":WAT:SOD:CLA", interval=1, entropy=1,
>
> /
>
> &gb
>
> igb=1, saltcon=0.100,
>
> /
>
> &decomp
>
> idecomp=1,
>
> dec_verbose=1,
>
> /
>
>
> I will be very thankful for the reply.
>
?Look at the _MMPBSA_complex_entropy.out file or any of the files with
"cpptrajentropy" in the name to look for a more complete error message.
Also note that quasi-harmonic analysis will typically require a LOT more
than 200 frames. It effectively does PCA and takes the mass-weighted
principal components as normal modes. And for PCA, you need at *least* 3x
more snapshots as you have atoms just to get enough eigenmodes. And you
typically need a lot more to converge your entropy.
I suggest reviewing literature on the quasi-harmonic approximation before
trying to use it (or interpret results coming from it).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 7
Date: Thu, 16 Apr 2015 16:14:21 +0200
From: gepaula.web.de
Subject: [AMBER] Writing out restart files
To: amber.ambermd.org
Message-ID:
<trinity-85b93050-8a75-424f-a20f-ac11776a9ab1-1429193661134.3capp-webde-bs21>
Content-Type: text/plain; charset="UTF-8"
Hello,
i have run a md simulation over 5 ns and wrote out a crd file. Now i want to
retrieve the restart-file of a single structure within that crd file. Can
anyone tell me how i can do this ?
Thank you very much in advance,
Best regards,
Paula
------------------------------
Message: 8
Date: Thu, 16 Apr 2015 08:27:33 -0600
From: Christina Bergonzo <cbergonzo.gmail.com>
Subject: Re: [AMBER] Writing out restart files
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAMLwDJ0FfH73kTDGy77sz6W2qHqOp7TcMqntAuK+P79K-Vdnag.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
You can use cpptraj to do this.
The Amber14 manual, page 502-505 details how to use trajin and trajout.
You'll want to use something like this, if you want for example frame 10:
$cpptraj << EOF
parm yourparm.parm7
trajin yourtraj.crd 10 10
trajout yourrst.rst restart
go
EOF
If you want to print multiple frames you can use the onlyframes command.
Hope this helps,
-Christina
On Thu, Apr 16, 2015 at 8:14 AM, <gepaula.web.de> wrote:
>
> Hello,
>
> i have run a md simulation over 5 ns and wrote out a crd file. Now i
> want to
> retrieve the restart-file of a single structure within that crd file.
> Can
> anyone tell me how i can do this ?
> Thank you very much in advance,
>
> Best regards,
> Paula
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
---------------------------------------------------------------------------------------
------------------------------
Message: 9
Date: Thu, 16 Apr 2015 08:30:47 -0600
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] Writing out restart files
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAAC0qOaYy5=aecBHOHE-ZJTsoYkKEMPnckhKYHXTmE5j-8SeRw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
In addition to what Christina said, be aware that unless you are using
a netcdf trajectory with velocities (or you use the mdvel keyword and
a trajectory containing velocity info) the restart will only have
coordinates.
-Dan
On Thu, Apr 16, 2015 at 8:27 AM, Christina Bergonzo <cbergonzo.gmail.com> wrote:
> Hi,
>
> You can use cpptraj to do this.
> The Amber14 manual, page 502-505 details how to use trajin and trajout.
>
> You'll want to use something like this, if you want for example frame 10:
>
> $cpptraj << EOF
> parm yourparm.parm7
> trajin yourtraj.crd 10 10
> trajout yourrst.rst restart
> go
> EOF
>
> If you want to print multiple frames you can use the onlyframes command.
>
> Hope this helps,
> -Christina
>
> On Thu, Apr 16, 2015 at 8:14 AM, <gepaula.web.de> wrote:
>
>>
>> Hello,
>>
>> i have run a md simulation over 5 ns and wrote out a crd file. Now i
>> want to
>> retrieve the restart-file of a single structure within that crd file.
>> Can
>> anyone tell me how i can do this ?
>> Thank you very much in advance,
>>
>> Best regards,
>> Paula
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ---------------------------------------------------------------------------------------
> Christina Bergonzo, PhD
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> 30 South 2000 East, Rm. 201
> Salt Lake City, UT 84112-5820
> Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652 / Fax: (801) 585-6208
> ---------------------------------------------------------------------------------------
> _______________________________________________
> 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: 10
Date: Thu, 16 Apr 2015 08:41:21 -0600
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] Evaluating hydrogen boding lifetime
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAAC0qObFGOGBPBxKYR2=UjJgCBz+dn2Nf=PKND1By0LrcFxPjQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
On Thu, Apr 16, 2015 at 12:41 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> Relating to hydrogen bonding calculations, now I would like to calculate
> the values for *water bridging*.
>
> Could you kindly brief me on how to calculate the number of bridging water
> from the HB calculation that I already done as indicated earlier mail in
> this post?
If you specified 'solventdonor' or 'solventacceptor' then the bridging
calculation is performed. It is written the file specified by
bridgeout, or solvout, or avgout (in order of precedence). If none of
that is specified it is written to STDOUT. See the manual for more
details.
-Dan
>
> Thanks
> Vijay
>
>
>
> On Tue, Mar 24, 2015 at 11:42 AM, Vijay Achari <glycoamber.gmail.com> wrote:
>
>> Dear Daniel,
>>
>> If you dont mind, could you provide the citation relevent for the
>> implementation of HB lifetime calcultion?
>>
>> Thanks in advance.
>>
>> Vijay
>>
>> On Sun, Mar 22, 2015 at 1:23 PM, Vijay Achari <glycoamber.gmail.com>
>> wrote:
>>
>>> Dear Daniel,
>>>
>>> I was away and now I am back.
>>>
>>> Thanks for your reply.
>>>
>>> Since I am working on disaccharide glycolipids, I have 11 acceptors
>>> (O11,O12,O13,O14,O15,O16,O22,O23,O24,O25,O26), and 7 hydroxyl groups
>>> (O12-H12, O13-H13, O16-H16, O22-H22, O23-H23, O24-H24, O26-H26).
>>>
>>> My main target was to know, in average, how long each acceptor (O) of a
>>> glycolipid involve in hydrogen bonding interaction no matter which donor is
>>> involved, in the glycolipid bilayer assembly.
>>>
>>> So to achieve this, I selected columns only with "O22" (for example:
>>> BMR_42.O22-BMR, BMR_49.O22-BMR, BMR_59.O22-BMR, BMR_23.O22-BMR,
>>> BMR_10.O22-BMR BMR_61.O22-BMR) and sum up all the "1s" and divided with
>>> the total number of frames involved. I repeated this procedure for each
>>> acceptors.
>>>
>>> If I am not mistaken, I guess what you have suggested is what I want
>>> actually. But I did not use *readdata* and *lifeltime* commands to get
>>> the final value. I used an awk script to do the selections column wise and
>>> average over all frames.
>>>
>>> Welcome any feedback from your side to enhance my understanding.
>>>
>>> Thank you.
>>> Vijay
>>>
>>>
>>>
>>>
>>> On Sun, Mar 22, 2015 at 12:06 AM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> You still haven't said whether I was right or wrong about you wanting
>>>> to calculate the lifetime of a certain solute atom (or residue) being
>>>> involved in *any* hydrogen bond. Since you haven't said no, I will
>>>> proceed on the assumption that this is what you want. In that case
>>>> this is the procedure I would use.
>>>>
>>>> 1) Calculate the hydrogen bond time series data (you have done this).
>>>>
>>>> 2) Use a script to sum up all columns involving your atom/residue of
>>>> interest. This could be as simple as visually identifying which
>>>> columns contain the data you need (e.g. columns 2, 4, 5, and 7) and
>>>> using something like awk:
>>>>
>>>> awk '{print $2 + $4 + $5 + $7}' solutehb.dat > sum.dat
>>>>
>>>> 3) Read the summed data back into cpptraj with readdata:
>>>>
>>>> readdata sum.dat
>>>>
>>>> 4) Perform lifetime analysis on the summed data. The default settings
>>>> for cutoff etc will still work since anything greater than 0 means a
>>>> hydrogen bond is present:
>>>>
>>>> lifetime sum.dat out life.sum.dat ...
>>>>
>>>> -Dan
>>>>
>>>> On Mon, Mar 16, 2015 at 10:50 AM, Vijay Achari <glycoamber.gmail.com>
>>>> wrote:
>>>> > Dear Dan,
>>>> >
>>>> > Below is the example you gave to explain on how the calculation of HB
>>>> can
>>>> > done with raw data.
>>>> >
>>>> >
>>>> > HB1-1 HB1-2
>>>> > 1 0
>>>> > 0 1
>>>> > 1 0
>>>> > 1 1
>>>> >
>>>> > Using the method I illustrated before you'd come up with an average of
>>>> > (5 / 4 = 1.25). However, the actual answer of how often is HB1
>>>> > involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
>>>> > is broken, HB1-2 is formed, so its always involved in some kind of
>>>> > hydrogen bond. So to do what you want you will need to write out the
>>>> > raw time series data, sum up the columns corresponding to the hydrogen
>>>> > bonds you are interested in, then run 'lifetime' analysis on that data
>>>> > set. So using the above sets as an example, the set I would actually
>>>> > run lifetime analysis on would look like:
>>>> >
>>>> >
>>>> > Relating to the above example, I understand that we need to add the
>>>> "1"s
>>>> > and divide by total number of lines.
>>>> >
>>>> > (total of all "1"s) / (total rows with "1"s)
>>>> >
>>>> >
>>>> > So how with the example below? (I modified the above sample).
>>>> >
>>>> > HB1-1 HB1-2
>>>> > 1 0
>>>> > 0 1
>>>> > 1 0
>>>> > 1 1
>>>> > 0 1
>>>> > 0 0
>>>> > 0 0
>>>> >
>>>> > For the above example is the the average is 6/7 or 6/5. The number 7
>>>> > stand for total number of rows and the later stand for rows with the
>>>> > presence of "1" (at least once).
>>>> >
>>>> > Means do I need to count the total rows or the rows with the
>>>> occurrence of
>>>> > "1" only?
>>>> >
>>>> >
>>>> >
>>>> > Your explanation would help me to write the script.
>>>> >
>>>> > Thanks.
>>>> >
>>>> >
>>>> >
>>>> > On Thu, Mar 12, 2015 at 4:53 PM, Vijay Achari <glycoamber.gmail.com>
>>>> wrote:
>>>> >
>>>> >> Dear Dan,
>>>> >>
>>>> >> Following your explanation, I would like to verify few things.
>>>> >>
>>>> >> #1) The file that contains the raw data; is this one "solutehb.dat"
>>>> >>
>>>> >> if yes,
>>>> >>
>>>> >> #2) The format of the data in the file is as below?
>>>> >>
>>>> >> #Frame *BMR_42.O22-BMR_1.O23-H23* BMR_49.O13-BMR_1.O13-H13
>>>> >> BMR_59.O13-BMR_2.O22-H22 BMR_10.O13-BMR_2.O26-H26 BMR_61.O26-BMR_3
>>>> .O22-H22
>>>> >> BMR_23.
>>>> >> O25-BMR_4.O12-H12 BMR_23.O26-BMR_4.O13-H13 BMR_23.O25-BMR_4.O13-H13
>>>> >> BMR_20.O13-BMR_5.O22-H22 BMR_10.O24-BMR_6.O13-H13 BMR_41.O23-BMR_7
>>>> .O23-H2
>>>> >> 3 BMR_41.O24-BMR_7.O23-H23 ....
>>>> >>
>>>> >>
>>>> >> * 1 * 1
>>>> >> 1 1 1
>>>> >> 1 1 1
>>>> >> 1 1 1
>>>> >> 1 1 1
>>>> >> 1 1 1
>>>> >> 1 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1
>>>> >> 1 1 1 . . .
>>>> >>
>>>> >>
>>>> >> #3) So need I operate on this file?
>>>> >>
>>>> >> #4) Is the first data "BMR_42.O22-BMR_1.O23-H23" is corresponding to
>>>> the
>>>> >> value "1" (below #2)
>>>> >>
>>>> >> Thank you.
>>>> >>
>>>> >>
>>>> >>
>>>> >>
>>>> >> On Wed, Mar 11, 2015 at 11:11 PM, Daniel Roe <daniel.r.roe.gmail.com>
>>>> >> wrote:
>>>> >>
>>>> >>> Hi,
>>>> >>>
>>>> >>> Sorry, it's not clear to me what you're trying to calculate. You said
>>>> >>> "I want to know the lifetime of HB for O22 (ACCEPTOR) atom only"; do
>>>> >>> you want the average lifetime of any given O22 involved in a hydrogen
>>>> >>> bond? In that case you will probably need to write your own script
>>>> for
>>>> >>> it for the time being. I'll try to illustrate why with an example.
>>>> Say
>>>> >>> I want to ask how often is BMR_49.O22 involved in any hydrogen bond
>>>> as
>>>> >>> an acceptor. I could naively sum up the total number of frames the
>>>> >>> bond is present (TotFrames) for each instance of this acceptor atom
>>>> >>> and then divide by the total number of lifetimes:
>>>> >>>
>>>> >>> 4 20 5 1.8500 37
>>>> >>> BMR_49.O22-BMR_1.O26-H26
>>>> >>> 7 28 2 1.0357 29
>>>> >>> BMR_49.O22-BMR_1.O13-H13
>>>> >>>
>>>> >>> the total number frames there is a hydrogen bond is 66, and the total
>>>> >>> number of lifetimes is 48, so the average lifetime for BMR_49.O22
>>>> >>> involved in any hydrogen bond (given the data here) is 1.375 frames.
>>>> >>> However, this is only true if the data were sequential, because it
>>>> >>> doesn't take into account the times when one is present and the other
>>>> >>> isn't. For example, given this hydrogen bond data (where HB1
>>>> >>> represents a single acceptor):
>>>> >>>
>>>> >>> HB1-1 HB1-2
>>>> >>> 1 0
>>>> >>> 0 1
>>>> >>> 1 0
>>>> >>> 1 1
>>>> >>>
>>>> >>> Using the method I illustrated before you'd come up with an average
>>>> of
>>>> >>> (5 / 4 = 1.25). However, the actual answer of how often is HB1
>>>> >>> involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
>>>> >>> is broken, HB1-2 is formed, so its always involved in some kind of
>>>> >>> hydrogen bond. So to do what you want you will need to write out the
>>>> >>> raw time series data, sum up the columns corresponding to the
>>>> hydrogen
>>>> >>> bonds you are interested in, then run 'lifetime' analysis on that
>>>> data
>>>> >>> set. So using the above sets as an example, the set I would actually
>>>> >>> run lifetime analysis on would look like:
>>>> >>>
>>>> >>> (HB1-1)+(HB1-2)
>>>> >>> 1
>>>> >>> 1
>>>> >>> 1
>>>> >>> 2
>>>> >>>
>>>> >>> Hope this helps,
>>>> >>>
>>>> >>> -Dan
>>>> >>>
>>>> >>> On Wed, Mar 11, 2015 at 12:57 AM, Vijay Achari <glycoamber.gmail.com
>>>> >
>>>> >>> wrote:
>>>> >>> > Dear Dan,
>>>> >>> >
>>>> >>> > In my case the time gap in between two frames (taken for analysis)
>>>> is
>>>> >>> 5ps.
>>>> >>> >
>>>> >>> > #Set Nlifetimes MaxLT AvgLT TotFrames SetName
>>>> >>> > 0 17 215 55.7059 947
>>>> >>> > BMR_42.O22-BMR_1.O23-H23
>>>> >>> > 1 1 1 1.0000 1
>>>> >>> > BMR_42.O23-BMR_1.O23-H23
>>>> >>> > 2 31 3 1.0968 34
>>>> >>> > BMR_31.O22-BMR_1.O26-H26
>>>> >>> > 3 11 2 1.0909 12
>>>> >>> > BMR_31.O13-BMR_1.O26-H26
>>>> >>> > 4 20 5 1.8500 37
>>>> >>> > BMR_49.O22-BMR_1.O26-H26
>>>> >>> > 5 24 4 1.7917 43
>>>> >>> > BMR_49.O23-BMR_1.O26-H26
>>>> >>> > 6 41 2 1.0488 43
>>>> >>> > BMR_49.O12-BMR_1.O12-H12
>>>> >>> > 7 28 2 1.0357 29
>>>> >>> > BMR_49.O22-BMR_1.O13-H13
>>>> >>> > 8 1 1000 1000.0000 1000
>>>> >>> > BMR_49.O13-BMR_1.O13-H13
>>>> >>> > 9 1 1 1.0000 1
>>>> >>> > BMR_22.O12-BMR_2.O22-H22
>>>> >>> > 10 50 62 18.9400 947
>>>> >>> > BMR_59.O13-BMR_2.O22-H22
>>>> >>> > 11 1 1 1.0000 1
>>>> >>> > BMR_59.O25-BMR_2.O23-H23
>>>> >>> > 12 34 5 1.1471 39
>>>> >>> > BMR_59.O13-BMR_2.O23-H23
>>>> >>> > 13 7 6 2.1429 15
>>>> >>> > BMR_59.O26-BMR_2.O24-H24
>>>> >>> > 14 6 8 3.6667 22
>>>> >>> > BMR_59.O25-BMR_2.O24-H24
>>>> >>> > 15 28 2 1.1071 31
>>>> >>> > BMR_10.O26-BMR_2.O26-H26
>>>> >>> > 16 52 121 15.1346 787
>>>> >>> > BMR_10.O25-BMR_2.O26-H26
>>>> >>> > 17 65 9 1.9231 125
>>>> >>> > BMR_10.O13-BMR_2.O26-H26
>>>> >>> > 18 4 4 2.2500 9
>>>> >>> > BMR_59.O26-BMR_2.O26-H26
>>>> >>> > 19 9 1 1.0000 9
>>>> >>> > BMR_22.O15-BMR_2.O13-H13
>>>> >>> > 20 1 1 1.0000 1
>>>> >>> > BMR_10.O11-BMR_2.O16-H16
>>>> >>> > 21 7 2 1.1429 8
>>>> >>> > BMR_53.O13-BMR_2.O16-H16
>>>> >>> > 22 2 3 2.5000 5
>>>> >>> > BMR_33.O13-BMR_3.O22-H22
>>>> >>> > 23 97 54 6.8247 662
>>>> >>> > BMR_61.O26-BMR_3.O22-H22
>>>> >>> > 24 1 1 1.0000 1
>>>> >>> > BMR_29.O26-BMR_3.O23-H23
>>>> >>> > 25 31 36 3.3226 103
>>>> >>> > BMR_29.O16-BMR_3.O23-H23
>>>> >>> > 26 22 2 1.2273 27
>>>> >>> > BMR_30.O22-BMR_3.O23-H23
>>>> >>> > 27 4 1 1.0000 4
>>>> >>> > BMR_33.O22-BMR_3.O23-H23
>>>> >>> > 28 38 2 1.1316 43
>>>> >>> > BMR_33.O13-BMR_3.O23-H23
>>>> >>> > (there are more than 2000 lines, but I work on only 28 lines to
>>>> get some
>>>> >>> > understanding)
>>>> >>> >
>>>> >>> >
>>>> >>> > For clarity, I shall show you how I worked on the given results
>>>> above.
>>>> >>> >
>>>> >>> > I want to know the lifetime of HB for O22 (ACCEPTOR) atom only.
>>>> So, I
>>>> >>> did
>>>> >>> > in this way,
>>>> >>> >
>>>> >>> > 1) sum the values from column AvgLT for the only occurrences of
>>>> O22.
>>>> >>> > 2) than find the average of that, where the denominator would be
>>>> the
>>>> >>> number
>>>> >>> > of occurrences of O22.
>>>> >>> >
>>>> >>> > Based on the above steps, the results are :
>>>> >>> >
>>>> >>> > O22 occur 6 times,
>>>> >>> > sum of O22 is 61.916, and
>>>> >>> > average of O22 is 10.319.
>>>> >>> >
>>>> >>> > So, I figured out the lifetime of O22 would be 10.319 x 5ps =
>>>> 51.595
>>>> >>> ps.
>>>> >>> >
>>>> >>> > Is this correct? Did I choose the correct column "AvgLT"?
>>>> >>> >
>>>> >>> > I hope to get some feedback if this is correct way to do it.
>>>> >>> >
>>>> >>> > Many thanks in advance.
>>>> >>> >
>>>> >>> > Vijay
>>>> >>> >
>>>> >>> >
>>>> >>> > On Wed, Mar 11, 2015 at 11:50 AM, Daniel Roe <
>>>> daniel.r.roe.gmail.com>
>>>> >>> wrote:
>>>> >>> >
>>>> >>> >> On Tue, Mar 10, 2015 at 9:24 PM, Vijay Achari <
>>>> glycoamber.gmail.com>
>>>> >>> >> wrote:
>>>> >>> >> > Could you explain on how to get the lifetime value in pico
>>>> second
>>>> >>> (ps)?
>>>> >>> >>
>>>> >>> >> This depends on how often you recorded your coordinate
>>>> trajectory. For
>>>> >>> >> example, say you ran a simulation with a timestep of 2 fs
>>>> (dt=0.002
>>>> >>> >> ps) and you recorded a trajectory frame every 500 steps
>>>> (ntwx=500).
>>>> >>> >> This means that each frame in your trajectory has been recorded
>>>> at 1
>>>> >>> >> ps intervals. However, say you recorded your trajectory every 5000
>>>> >>> >> steps instead - your trajectory then will have been recorded at
>>>> 10 ps
>>>> >>> >> intervals. Since lifetimes are always given in frames, it should
>>>> be
>>>> >>> >> easy to convert to ps based on how often your coordinate
>>>> trajectory
>>>> >>> >> was written to (e.g. in the latter case a max lifetime of 1 frame
>>>> >>> >> would mean 10 ps).
>>>> >>> >>
>>>> >>> >> Hope this helps,
>>>> >>> >>
>>>> >>> >> -Dan
>>>> >>> >>
>>>> >>> >> >
>>>> >>> >> > Thanks in advance.
>>>> >>> >> > Vijay
>>>> >>> >> >
>>>> >>> >> >
>>>> >>> >> > On Tue, Mar 10, 2015 at 10:15 PM, Daniel Roe <
>>>> daniel.r.roe.gmail.com
>>>> >>> >
>>>> >>> >> wrote:
>>>> >>> >> >
>>>> >>> >> >> Hi,
>>>> >>> >> >>
>>>> >>> >> >> On Tue, Mar 10, 2015 at 2:53 AM, Vijay Achari <
>>>> glycoamber.gmail.com
>>>> >>> >
>>>> >>> >> >> wrote:
>>>> >>> >> >> > generate two files with lifetime information. The
>>>> >>> >> *solute.lifetime.dat*
>>>> >>> >> >> contain
>>>> >>> >> >> > info like:
>>>> >>> >> >> >
>>>> >>> >> >> > #Set Nlifetimes MaxLT AvgLT TotFrames
>>>> SetName
>>>> >>> >> >> > 0 22 1 1.0000
>>>> 22
>>>> >>> >> >> BMR_3.O16-BMR_1.O22-H22
>>>> >>> >> >> > 1 296 346 15.6959 4646
>>>> >>> >> >> BMR_42.O22-BMR_1.O22-H22
>>>> >>> >> >> > 2 992 12 1.4688
>>>> 1457
>>>> >>> >> >> BMR_42.O14-BMR_1.O22-H22
>>>> >>> >> >> > 3 1 1 1.0000
>>>> 1
>>>> >>> >> >> BMR_42.O13-BMR_1.O22-H22
>>>> >>> >> >> > 4 189 12 1.1429
>>>> 216
>>>> >>> >> >> BMR_57.O25-BMR_1.O22-H22
>>>> >>> >> >> > 5 462 410 12.3074 5686
>>>> >>> >> >> BMR_57.O16-BMR_1.O22-H22
>>>> >>> >> >> >
>>>> >>> >> >> > I would like to know how I can go from here to calculate the
>>>> >>> >> hb-lifetime
>>>> >>> >> >> between
>>>> >>> >> >> > solute and solute?
>>>> >>> >> >>
>>>> >>> >> >> I'm not really sure I understand your question. The data
>>>> output you
>>>> >>> >> >> posted is exactly the lifetime calculation. For example, the
>>>> second
>>>> >>> >> >> set (1) contains lifetime information for the hydrogen bond
>>>> between
>>>> >>> >> >> residue 42, atom O22 and residue 1, atoms O22-H22; there were
>>>> 296
>>>> >>> >> >> individual lifetimes (i.e. the hbond formed 296 times), the
>>>> max of
>>>> >>> >> >> which lasted 346 frames, the average lifetime is ~15.7 frames.
>>>> Let
>>>> >>> me
>>>> >>> >> >> know if I'm not understanding you or if I can explain more.
>>>> >>> >> >>
>>>> >>> >> >> -Dan
>>>> >>> >> >>
>>>> >>> >> >> >
>>>> >>> >> >> > I have read the pages 556-557 from AMBER 14 manual, but I
>>>> find it
>>>> >>> >> >> difficult
>>>> >>> >> >> > to see how one should start processing and getting the
>>>> lifetime
>>>> >>> value.
>>>> >>> >> >> >
>>>> >>> >> >> > I think simple example would help me much in this case.
>>>> >>> >> >> >
>>>> >>> >> >> > Could you give me some example on how this can be obtained?
>>>> >>> >> >> >
>>>> >>> >> >> > Your help is much appreciated.
>>>> >>> >> >> >
>>>> >>> >> >> > Thank you.
>>>> >>> >> >> > 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
>>>> >>> >> >>
>>>> >>> >> > _______________________________________________
>>>> >>> >> > 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)
>>>> >>>
>>>> >>> _______________________________________________
>>>> >>> 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: 11
Date: Thu, 16 Apr 2015 10:20:43 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Writing out restart files
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3pjdCMHzRV_hmQwCQm=7MbsC=0QGZK7sMdtsRuib89ZNA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On Thu, Apr 16, 2015 at 10:14 AM, <gepaula.web.de> wrote:
>
> Hello,
>
> i have run a md simulation over 5 ns and wrote out a crd file. Now i
> want to
> retrieve the restart-file of a single structure within that crd file.
> Can
> anyone tell me how i can do this ?
>
?cpptraj can do this. Note that unless you also saved velocities in your
trajectory file (by setting ntwv=-1 in your input file), your restart will
have no velocities.
Also, unless you set ioutfm=1 (NetCDF trajectories) in your input file, the
ASCII trajectory format has *much* lower precision, and your restart files
will be limited to 3 decimal places of precision for each of the
coordinates.
In cpptraj, you would read in the frame you want to turn into a restart,
then write it out as a restart:
trajin my_trajectory
trajout my_restart restart onlyframes <frame>
Where <frame> is the frame you want to print.
HTH,
Jason
?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 12
Date: Thu, 16 Apr 2015 08:44:41 -0600
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] Diffusion constant calculation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAAC0qObD8JxKnqf+Q-Tpgz+sejAtTTdkN8Atqe6n0zAy48VrTw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
Amber 12 is a few years old at this point. I recommend upgrading to
AmberTools 14 and trying again - the 'unwrap' action in cpptraj was
vastly improved after AmberTools 12.
-Dan
On Wed, Apr 15, 2015 at 9:42 PM, pooja chahal <chahal.pooja.rs.gmail.com> wrote:
> Hi,
>
> I am using cpptraj (AMBER 12 version ). The input file for cpptraj that I
> am using is as follow:
>
> trajin traj1
> trajin traj2
> unwrap
> trajout x.out pdb multi nobox
>
> I am getting following error:
>
> ACTIONS: Initializing 1 actions:
> 0: [unwrap]
> PTRAJ ACTION: [unwrap]
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> PARM [abc.parm7]: Setting up 1 actions.
> 0: [unwrap]
> Mask [*] represents 23012 atoms
> UNWRAP
> The atoms in the calculation follow: * (All atoms are selected)
> ----- [abc_prod1.mdcrd] (1-1000, 1) -----
> 0% Warning: Action [unwrap] failed, frame 0.
>
>
> On Wed, Apr 15, 2015 at 10:43 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> On Wed, Apr 15, 2015 at 6:25 AM, pooja chahal <chahal.pooja.rs.gmail.com>
>> wrote:
>> > Thanks for the reply. I have tried cpptraj following your suggestion but
>> I
>> > am unable to unwrap the trajectory using cpptraj. I have no prior
>> > experience of using cpptraj. Also asterisks are not observed in the
>> > original ASCII trajectory file. As I have mentioned earlier, I have used
>> > iwrap=1 during my production run.
>>
>> Could you provide some more detail on how you were unable to unwrap
>> with cpptraj? Does it not recognize the command? Does it give an error
>> message? What version of cpptraj have you tried?
>>
>> -Dan
>>
>> >
>> > On Tue, Apr 14, 2015 at 7:36 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >
>> >> Hi,
>> >>
>> >> On Mon, Apr 13, 2015 at 10:42 PM, pooja chahal
>> >> <chahal.pooja.rs.gmail.com> wrote:
>> >> > Also one more thing that I am observing is that while generating .pdb
>> >> files
>> >> > using ptraj with unwrap command, some of atoms attains a very high
>> >> negative
>> >> > value (< -1000) for coordinates. For these coordinates "********"
>> appears
>> >> > in the .pdb file instead of real coordinates. However, this is not the
>> >> only
>> >>
>> >> This seems odd to me. The multiple asterisks is something that fortran
>> >> code does for numerical overflow, not C/C++ code (to my knowledge).
>> >> You shouldn't be getting asterisks in your PDB files if you're
>> >> creating them with ptraj. Do you get the same behavior with cpptraj?
>> >>
>> >> If on the other hand you mean you see asterisks in the original ASCII
>> >> trajectory file then your coordinates overflowed during your
>> >> simulation and there is no way to recover them. For this reason it is
>> >> recommended that during simulations you use 'iwrap=1' to enable
>> >> imaging, 'ioutfm=1' to write NetCDF trajectories, and 'ntxo=2' to
>> >> write NetCDF restart files; the NetCDF file format is not nearly as
>> >> susceptible to issues as the ASCII format.
>> >>
>> >> Hope this helps,
>> >>
>> >> -Dan
>> >>
>> >> --
>> >> -------------------------
>> >> 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)
>>
>> _______________________________________________
>> 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: 13
Date: Thu, 16 Apr 2015 19:20:45 +0430
From: Atila Petrosian <atila.petrosian.gmail.com>
Subject: [AMBER] all in one pc for MD simulation calculations
To: amber <amber.ambermd.org>
Message-ID:
<CAON_0oUvvhVUZm9THWM8XqpH=1orX0nd0J0L4rHJahAOe9By_g.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear amber users
I have a question about computer which is needed for MD simulation by amber.
Is an all in one pc appropriate for MD simulation?
Any help will highly appreciated.
------------------------------
Message: 14
Date: Thu, 16 Apr 2015 10:57:55 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] all in one pc for MD simulation calculations
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3o_H-uDRaL7M6esPWjh09x+4UP_=3BQ8vvxW=oAsq=rWQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On Thu, Apr 16, 2015 at 10:50 AM, Atila Petrosian <atila.petrosian.gmail.com
> wrote:
> Dear amber users
>
>
>
> I have a question about computer which is needed for MD simulation by
> amber.
>
>
>
> Is an all in one pc appropriate for MD simulation?
>
?Depends on the all-in-1 PC and what exactly you want to do with "MD". If
you want a GPU-accelerated machine, then you need to make sure that the PC
comes with a qualifying CUDA-capable GPU. A GTX 780 or 980 is best, while
the more budget versions (x70, x60, x50, ...) will be quite noticeably
slower.
Other than that consideration, there is no difference between an all-in-1
and a standard desktop (or laptop) when it comes to doing simulations --
what matters is the speed of the CPU and the speed and amount of the RAM
for the most part.
(And, of course, you have to delete Windoze and replace it with a good,
Unix-based operating system like a Linux or a BSD).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 15
Date: Thu, 16 Apr 2015 14:53:19 -0400
From: Laura Tociu <ltociu.princeton.edu>
Subject: [AMBER] NMode Analysis Using Truncated Trajectory
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CANThz_hT5Tp9Swit3Ota+_+m6=HOcDi0L9rvU9HDi7MEnuDO-g.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear all,
I am trying to calculate the free energy of binding of a ligand to a
protein that has around 6000 atoms. Needless to say running NMode on the
whole protein takes forever, the minimization gets stuck very frequently
and it also doesn't seem like the drms is going any lower after a while.
I am looking into truncating the trajectory using the method described here:
http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html
I would like to know if the code changes outlined there are still the code
changes that would be needed in the amber14 code. I am also unsure as to
why so many confusing steps seem to be needed for this to work.
Wouldn't taking the following steps be enough:
1) Determine which residues are within 12 angstroms of the ligand (I would
personally do this by using the VMD command same residue as within 12 of
ligand) and which are within 8 of the ligand in the same way.
2) Truncate the trajectory in cpptraj:
parm full_system.parm7
trajin full_system.nc
strip : "residues that are not within 12 of ligand" outprefix trunc
trajout trunc.nc netcdf
3) Change the mm_pbsa_createinput file so that it writes input files for
nmode in which the residues between 8 and 12 Angstroms are restrained.
4) Remove all the lines in leaprc.ff14SB under addPdbResMap. *--- Is this
really necessary? *Wouldn't we want the input files for NMode to consist of
the ligand + the residues within 12 Angstroms of it, capped nicely at their
loose ends? Or just the residues within 12 Angstroms of the ligand in the
case of the receptor, but with their loose ends capped nicely? Or is it
that by truncating the trajectory, the residues are not capped, in which
case there would be a disagreement between the number of atoms in the
topology file and that in the input files?
5) Make nmode able to run thermo analysis even if belly is used by:
In nmode.f (around line 296):
write(6,*) 'Thermo analysis not supported for belly calc.'
! Code added by Jacob Kongsted 2007 for new MM/PBSA entropy
! JK
nvecs = 3*natsys - 6
call thermo(natsys,nvecs,ilevel,x(mx),x(mamass),x(mcval), &
x(mh),x(mh+ns3),x(mh+2*ns3), &
x(mh+3*ns3),t,patm)
! End of new code
In make_crd_hg.f:
parameter (NMO=400)
Lastly, I am not sure why in the procedure I was referring to, the authors
were trying to include some water molecules in the buffer zone. Were those
crystallographic waters? Otherwise I am not sure why there would be waters
in the trajectory in the first place. Isn't the first thing that MM-PBSA
does to strip the trajectories of water molecules?
Thank you a lot!
Laura
------------------------------
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End of AMBER Digest, Vol 1191, Issue 1
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Received on Fri Apr 17 2015 - 09:00:02 PDT