Re: [AMBER] AMBER Digest, Vol 989, Issue 1

From: amirhossein taghavi <amirhosseintaghavi240.yahoo.com>
Date: Mon, 29 Sep 2014 00:42:41 -0700

Hi,

I removed the noimage from script and added the parmbox info plus the angles as you said and the problem is solved.Thanks a lot!
May I ask what do you mean by 'corner case' and how can I learn more about the algorithms that cpptraj uses to analyze bonds,dihedrals and ....

Thanks in Forward
Amir




On Friday, September 26, 2014 9:00 PM, "amber-request.ambermd.org" <amber-request.ambermd.org> wrote:
 


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AMBER Mailing List Digest

Today's Topics:

   1. Combined cartesian and NMR restraints (Parker de Waal)
   2. Re: Combined cartesian and NMR restraints (Parker de Waal)
   3. Re: Combined cartesian and NMR restraints (David A Case)
   4. Re: Combined cartesian and NMR restraints (Parker de Waal)
   5. US AMBER Workshop - Save the date (Ross Walker)
   6. cpptraj/parmbox (amirhossein taghavi)
   7. Re: bash scripting for MD tasks (James Starlight)
   8. Re: RMSD on two slightly different structures
      (Guillaume Roellinger)
   9. Re: bash scripting for MD tasks (James Starlight)
  10. Re: Combined cartesian and NMR restraints (Parker de Waal)
  11. Fw: Welcome to Beijing for the 15th International Congress of
      Quantum Chemistry (??)
  12. Re: cpptraj/parmbox (Jason Swails)
  13. Re: cpptraj/parmbox (Daniel Roe)
  14. Re: Combined cartesian and NMR restraints (Jason Swails)
  15. FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type
      (Soumendranath Bhakat)
  16. Re: FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type
      (Carlos Simmerling)
  17. Re: FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type
      (David A Case)
  18. Re: bash scripting for MD tasks (Ross Walker)
  19. Re: cpptraj/parmbox (Daniel Roe)


----------------------------------------------------------------------

Message: 1
Date: Fri, 26 Sep 2014 01:43:54 +0000
From: Parker de Waal <Parker.deWaal.vai.org>
Subject: [AMBER] Combined cartesian and NMR restraints
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID: <974700F6B71AA04897B9105CC7E1AAFA7B3256.VAIEXMB01.vai.org>
Content-Type: text/plain; charset="us-ascii"

Hello Everyone,

After reading through some of the old mailing list threads regarding the various workarounds for ntr =1 and nmropt=1, I still need some clarification.

I have an NVT prod.in as show below:

NVT prod
&cntrl
  irest=1, ntx =5,
  nstlim=5000000, dt=0.002,
  ntpr=500, ntwr=500, ntwx=500,
  temp0=300.0,
  ntt=3, gamma_ln=5, ntb=1, ntp=0,
  ntc=2, ntf=2, ig=-1,
  cut=9,
  ioutfm = 1,
  iwrap=1, nmropt=1,
  ntr=1,
&end
&wt type='END' /
DISANG=rst.dist

Now I wish to add cartesian restraints, following the snippet here: http://ambermd.org/Questions/constraints.html into my rst.dist file as seen below:

# N373 D69 VS
&rst
  ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
      rk2=0.0, rk3=25.0, ir6=1, ialtd=0,
&end
... (lines removed)
# A150 F244 VS
&rst
  ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
&end
Hold GPCR fixed
20.0
RES 1 708
END
END

However whenever I run this the follow error occurs:

   5. REFERENCE ATOM COORDINATES

  default_name
    ----- READING GROUP 1; TITLE:
DISANG=rst.dist

     rfree: End of file on unit 5

If someone could provide some input on how to achieve this I would greatly appreciate it.

Best,
Parker




------------------------------

Message: 2
Date: Fri, 26 Sep 2014 02:37:44 +0000
From: Parker de Waal <Parker.deWaal.vai.org>
Subject: Re: [AMBER] Combined cartesian and NMR restraints
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <974700F6B71AA04897B9105CC7E1AAFA7B32AA.VAIEXMB01.vai.org>
Content-Type: text/plain; charset="us-ascii"

Update:

A little ordering fixes everything! Both the harmonic restraints and distance restraints are being read and applied according to the out.file

NVT prod
&cntrl
  irest=1, ntx =5,
  nstlim=5000000, dt=0.002,
  ntpr=500, ntwr=500, ntwx=500,
  temp0=300.0,
  ntt=3, gamma_ln=5, ntb=1, ntp=0,
  ntc=2, ntf=2, ig=-1,
  cut=9,
  ioutfm = 1,
  iwrap=1, nmropt=1,
  ntr=1,
/
&wt type='END' /
DISANG=rst.dist
&end
Hold lipid fixed
10.0
RES 1 384
END
END

However now I'm encountering a new CUDA related problem:

Error: an illegal memory access was encountered launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered

Is it possible for one of the CUDA developers to provide insight into this?

Best,
Parker

________________________________________
From: Parker de Waal [Parker.deWaal.vai.org]
Sent: Thursday, September 25, 2014 9:43 PM
To: amber.ambermd.org
Subject: [AMBER] Combined cartesian and NMR restraints

Hello Everyone,

After reading through some of the old mailing list threads regarding the various workarounds for ntr =1 and nmropt=1, I still need some clarification.

I have an NVT prod.in as show below:

NVT prod
&cntrl
  irest=1, ntx =5,
  nstlim=5000000, dt=0.002,
  ntpr=500, ntwr=500, ntwx=500,
  temp0=300.0,
  ntt=3, gamma_ln=5, ntb=1, ntp=0,
  ntc=2, ntf=2, ig=-1,
  cut=9,
  ioutfm = 1,
  iwrap=1, nmropt=1,
  ntr=1,
&end
&wt type='END' /
DISANG=rst.dist

Now I wish to add cartesian restraints, following the snippet here: http://ambermd.org/Questions/constraints.html into my rst.dist file as seen below:

# N373 D69 VS
&rst
  ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
      rk2=0.0, rk3=25.0, ir6=1, ialtd=0,
&end
... (lines removed)
# A150 F244 VS
&rst
  ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
&end
Hold GPCR fixed
20.0
RES 1 708
END
END

However whenever I run this the follow error occurs:

   5. REFERENCE ATOM COORDINATES

  default_name
    ----- READING GROUP 1; TITLE:
DISANG=rst.dist

     rfree: End of file on unit 5

If someone could provide some input on how to achieve this I would greatly appreciate it.

Best,
Parker


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


------------------------------

Message: 3
Date: Thu, 25 Sep 2014 22:56:31 -0400
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] Combined cartesian and NMR restraints
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20140926025631.GB3304.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

On Fri, Sep 26, 2014, Parker de Waal wrote:
>
> After reading through some of the old mailing list threads regarding
> the various workarounds for ntr =1 and nmropt=1, I still need some
> clarification.
>
> I have an NVT prod.in as show below:
>
>
> Now I wish to add cartesian restraints, following the snippet here:
> http://ambermd.org/Questions/constraints.html into my rst.dist file as
> seen below:

The group cards for cartesian restraints go into the mdin file, not into the
restraints file.


>
> # N373 D69 VS
> &rst
> ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
> rk2=0.0, rk3=25.0, ir6=1, ialtd=0,
> &end
> ... (lines removed)
> # A150 F244 VS
> &rst
> ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
> &end
> Hold GPCR fixed
> 20.0
> RES 1 708
> END
> END
>
> However whenever I run this the follow error occurs:
>
> 5. REFERENCE ATOM COORDINATES
>
> default_name
> ----- READING GROUP 1; TITLE:
> DISANG=rst.dist

Note that the program thinks the DISANG card is the title for the cartesian
restraints; so somehow it is not reading the NMR-like restraints correctly.
The first thing you need to do is set ntr=0, and make sure that you are
getting the NMR restraints correctly processed. Follow the example in the
$AMBERHOME/test/nmr directory.

By far the simplest thing to do for cartsian restraints is to set them
in the cntrl namelist:

   ntr=1, restraint_wt=20., restraintmask=':1-708',

Then there is no need for any GROUP input.

Beyond this:

You could try using the correct "/" rather than the obsolete (and never
standard "&end" to end namelists. But that is probably not the source of the
problem. You may need to let us know which program you are running
(sander or pmemd?) and which version. Posting the entire mdout file is
probably also required...there is something subtle that is preventing your
file from being parsed correctly.

....dac



------------------------------

Message: 4
Date: Fri, 26 Sep 2014 03:26:14 +0000
From: Parker de Waal <Parker.deWaal.vai.org>
Subject: Re: [AMBER] Combined cartesian and NMR restraints
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <974700F6B71AA04897B9105CC7E1AAFA7B32E4.VAIEXMB01.vai.org>
Content-Type: text/plain; charset="us-ascii"

Hi David,

Thank you for the input. I've adjusted the input per your suggestion as follows:

NVT prod
&cntrl
  irest=1, ntx =5,
  nstlim=5000000, dt=0.002,
  ntpr=500, ntwr=500, ntwx=500,
  temp0=300.0,
  ntt=3, gamma_ln=5, ntb=1, ntp=0,
  ntc=2, ntf=2, ig=-1,
  cut=9,
  ioutfm = 1,
  iwrap=1, nmropt=1,
  ntr=1, restraint_wt=20., restraintmask=':1-708',
/
&wt type='END' /
DISANG=rst.dist

The only problem now is that when I run pmemd.CUDA the follow error occurs:
Error: an illegal memory access was encountered launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered

I'm currently using the most recent version of AMBER14 (updated and recompiled today) with NVIDIA Driver Version: 340.32 and Cuda compilation tools, release 6.5, V6.5.12 (I'm running arch so rolling back is difficult, but I'm trying now to 5.5)

Parker

________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Thursday, September 25, 2014 10:56 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Combined cartesian and NMR restraints

On Fri, Sep 26, 2014, Parker de Waal wrote:
>
> After reading through some of the old mailing list threads regarding
> the various workarounds for ntr =1 and nmropt=1, I still need some
> clarification.
>
> I have an NVT http://scanmail.trustwave.com/?c=129&d=49Wk1K_bbQBiQ3IZT3Q0OKQyeRAK9WcrWuJ7VB2iCg&u=http%3a%2f%2fprod%2ein as show below:
>
>
> Now I wish to add cartesian restraints, following the snippet here:
> http://scanmail.trustwave.com/?c=129&d=49Wk1K_bbQBiQ3IZT3Q0OKQyeRAK9WcrWuUuUBb1CQ&u=http%3a%2f%2fambermd%2eorg%2fQuestions%2fconstraints%2ehtml into my rst.dist file as
> seen below:

The group cards for cartesian restraints go into the mdin file, not into the
restraints file.


>
> # N373 D69 VS
> &rst
> ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
> rk2=0.0, rk3=25.0, ir6=1, ialtd=0,
> &end
> ... (lines removed)
> # A150 F244 VS
> &rst
> ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
> &end
> Hold GPCR fixed
> 20.0
> RES 1 708
> END
> END
>
> However whenever I run this the follow error occurs:
>
> 5. REFERENCE ATOM COORDINATES
>
> default_name
> ----- READING GROUP 1; TITLE:
> DISANG=rst.dist

Note that the program thinks the DISANG card is the title for the cartesian
restraints; so somehow it is not reading the NMR-like restraints correctly.
The first thing you need to do is set ntr=0, and make sure that you are
getting the NMR restraints correctly processed. Follow the example in the
$AMBERHOME/test/nmr directory.

By far the simplest thing to do for cartsian restraints is to set them
in the cntrl namelist:

   ntr=1, restraint_wt=20., restraintmask=':1-708',

Then there is no need for any GROUP input.

Beyond this:

You could try using the correct "/" rather than the obsolete (and never
standard "&end" to end namelists. But that is probably not the source of the
problem. You may need to let us know which program you are running
(sander or pmemd?) and which version. Posting the entire mdout file is
probably also required...there is something subtle that is preventing your
file from being parsed correctly.

....dac

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://scanmail.trustwave.com/?c=129&d=5NWk1DkJ-rwIWc9WjII5xYe7GxkTZDMTXvE-6uITXQ&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinfo%2famber


------------------------------

Message: 5
Date: Thu, 25 Sep 2014 21:27:26 -0700
From: Ross Walker <ross.rosswalker.co.uk>
Subject: [AMBER] US AMBER Workshop - Save the date
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <D04A393E.49A71%ross.rosswalker.co.uk>
Content-Type: text/plain; charset="US-ASCII"

Dear All

This is a provisional note that we are considering running an AMBER
Workshop in conjunction with the NBCR and NVIDIA at the University of
California San Diego. The provisional dates are Dec 15th to the 18th.

This is tentative at present but I wanted to give those interested a heads
up to save these dates if interested.

More details to follow.

All the best
Ross

/\
\/
|\oss Walker

---------------------------------------------------------
| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.









------------------------------

Message: 6
Date: Fri, 26 Sep 2014 00:13:59 -0700
From: amirhossein taghavi <amirhosseintaghavi240.yahoo.com>
Subject: [AMBER] cpptraj/parmbox
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID:
    <1411715639.51396.YahooMailNeo.web142405.mail.bf1.yahoo.com>
Content-Type: text/plain; charset=us-ascii

Hello everyone,

My rpoblem is not directly related to MD but as I use Amber cpptraj to analyze my data, I wondered may some one could have some help!!

I have a CG model of DNA in xyz format and I am using cpptraj to do some measurements on bonds,angles and dihedrals.The problem is, for example, when I calculate the base interdistances with piece of a script I have, in some frames the distance is calculated with the image of particle at the end of the box, like say my box is 136A. so if the usual BB distance is between 5-7A is some frames it jumps tp 136.
I have added parmbox information to the script but the problem still exists.
any help or suggestion is highly appreciated.

Thanks in Forward


------------------------------

Message: 7
Date: Fri, 26 Sep 2014 11:43:22 +0200
From: James Starlight <jmsstarlight.gmail.com>
Subject: Re: [AMBER] bash scripting for MD tasks
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
    <CAALQopwRPn2gfqRH6q3dZwfh17x3TPD2w=+zqWH19uo=TtXvRw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear all,

I wounder to ask some suggestions about possibility to improve my launch
script aimed on the running of several similations.

e.g my current protocol use simple looping over the dir with the
simulations to run sh file in each folder which is call for the pmemd etc
for each system

#!/bin/bash

# set workdir with proteins
dirr=/home/gleb/Documents/script
simulations=/home/gleb/Documents/script/Simulations



#run each simulation
for sim in $simulations/* ; do
  simulation=$(basename "$sim")
  echo "Simulation of ${simulation} is in a progress!"
  cd $sim
  chmod +x ./${simulation}.Sh
  ./${simulation}.Sh
  echo "Simulation of ${simulation} has been finished"
done

how this script can be improved to i) avoid call sh from the another sh?
ii) to run several jobs in parallel corresponded to the number of available
GPU of my workstation ?

Thanks for help,

James


------------------------------

Message: 8
Date: Fri, 26 Sep 2014 10:56:30 +0000
From: Guillaume Roellinger <roellinger.bio.mx>
Subject: Re: [AMBER] RMSD on two slightly different structures
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <1411728990911.30184.bio.mx>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

Thanks a lot! I was indeed using an older version of cpptraj (14.01). I updated and recompiled and it is working now.
I took a deeper look at my output and just as you said both masks are processed: the reference mask when the action is initialized and the target mask in the 'ACTION SETUP FOR PARM' section during processing, so it was working as well.

Thank you for your help!

Best,

Guillaume

________________________________________
Von: Daniel Roe <daniel.r.roe.gmail.com>
Gesendet: Donnerstag, 25. September 2014 17:14
An: AMBER Mailing List
Betreff: Re: [AMBER] RMSD on two slightly different structures

Hi,

What version of cpptraj are you using? It should be 14.09. The
segfault you describe sounds a lot like an issue that was fixed in
update 6 for AmberTools 14.

On Thu, Sep 25, 2014 at 2:39 AM, Guillaume Roellinger <roellinger.bio.mx> wrote:
> About Daniel's answer:
>
> The statement [rms reference :1-265.CA :6-270.CA] works however I have no idea how cpptraj knows which mask is related to which structure. I tried to add parmindex for each mask but it did not work. Switching both masks did not work [rms reference :6-270.CA :1-265.CA] and the output let me think that only the first mask is taken into account and the second mask is just ignored:
> [0: [rms reference :1-265.CA :6-270.CA out RMSD.dat]
> Mask [:1-265.CA] corresponds to 265 atoms.]

Both masks are processed. The first mask is always the target mask,
and the second mask is always the reference mask (as stated in the
manual). The reference mask for 'reference' is processed when the
action is initialized (near the top of your output). The target mask
is processed in the 'ACTION SETUP FOR PARM' section during processing,
which is what you were reporting.

> It would then explain why the mask switching did not work: if only the first mask matters, it is looking in both structures for :6-270.CA. In the structure with 271 residues, the masks corresponds to more atoms than in the second structure with 265 residues. Mismatch in the number of atom will cause rms to fail.

Without seeing your entire output I can't be sure what is happening.
Can you send it in an email or as an attachment?

-Dan

>
> Best regards,
>
> Guillaume
>
>
> ___________________________________
> Von: Jason Swails <jason.swails.gmail.com>
> Gesendet: Montag, 22. September 2014 14:23
> An: amber.ambermd.org
> Betreff: Re: [AMBER] RMSD on two slightly different structures
>
> On Mon, 2014-09-22 at 07:18 +0000, Guillaume Roellinger wrote:
>> Dear all,
>>
>>
>> Using cpptraj, I am computing the RMSD between two almost similar
>> structures with two different topology files and then perform a PCA.
>> Structure A has 265 residues and structure B: 271. The sequence in
>> structure A from residue 1 to 265 is the almost the same (there are
>> 2-3 mutations) as in structure B from residue 5 to 270.
>
> Note that there is 1 more residue between residues 5 and 270 compared to
> residues 1 to 265. I'll assume you really meant 6 to 270 (so the first
> 5 residues are different) in the rest of my answer.
>>
>> I am computing the RMSD this way and it is working:
>>
>> parm structureA.prmtop
>> parm structureB.prmtop
>> trajin structureA.pdb parmindex 0
>> trajin structureB.pdb parmindex 1
>> reference structureA.pdb parmindex 0
>> rms reference :1-265.CA
>>
>> 1st question: When I am selecting the residue range 1-265, does it
>> take from both structure A and B the residues 1 to 265 or does it
>> select from structure A residues 1 to 265 and from structure B
>> residues 5 to 270 (=the almost common sequence part)?
>
> It selects both 1 to 265 of both residues. If you want to select
> residues 6 to 270 of the reference structure, you should provide that
> mask to the reference statement. For example, change the reference
> command to:
>
> reference structureA.pdb parmindex 0 :6-270
>
> This will bring in the 265 residues starting from residue 6 (and they
> should be renumbered sequentially starting from 1).
>
>>
>> 2nd question (related to the first one): In an other example, I have
>> structures C with 278 residues and D with 277. What appends if I have
>> "gaps" in both sequences and if I compute the RMSD with :1-277.CA as
>> mask (this is working as well!) ?
>
> cpptraj does not recognize "gaps" by default. You may want to look into
> the "atommap" command, which may help you create a mapping between the
> two structures you want to compare.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> 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: 9
Date: Fri, 26 Sep 2014 13:14:05 +0200
From: James Starlight <jmsstarlight.gmail.com>
Subject: Re: [AMBER] bash scripting for MD tasks
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
    <CAALQopxgz84uJ2D7g598OFykvDFzcvVLzvV5sWUVBuHtBkbgAA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
The general idea here to avoid palatalization and just run jobs still being
in loop using 2 variables one corresponded to the looping over GPUs iDs and
the second to the folder of each simulation.
Below you could find two examples (unfortunately both still incomplete
because I'm not an expert in BASH)
#!/bin/bash
# set workdir with proteins
dirr=/home/gleb/Documents/script
simulations=/home/gleb/Documents/script/Simulations
#run each simulation in parallel using nested loop which might not be good
solution : here the problem that some condition should be provided to avoid
using >1 simulation on the same GPU
#
i=0 # the number of first GPU which will be used!
while i < n ; do # the maximum number of the available GPUs on the machines
# m.b n also might be obtained using some command ?
# !!!!some condition should be specified to pass sharing SAME GPU between
different md runs !!!
export CUDA_VISIBLE_DEVICES "$i"
for sim in $simulations/* ; do
   simulation=$(basename "$sim")
   echo "Simulation of ${simulation} is in a progress on ${i} GPU!!"
   cd $sim
   chmod +x ./${simulation}.Sh
  ./${simulation}.Sh &
   echo "Simulation of ${simulation} has been finished"
  done
done
# alternatively possibility to do the same taks using 2 variables within
one FOR loop-> here we must have the same number of the GPUs and MD jobs.
for i in {0..$n},  sim in $simulations/* ; do # it seems that problem here
in the syntax!!!
  export CUDA_VISIBLE_DEVICES "$i"
  simulation=$(basename "$sim")
  echo "Simulation of ${simulation} is in a progress on ${i} GPU!"
  cd $sim
  chmod +x ./${simulation}.Sh
./${simulation}.Sh &
  echo "Simulation of ${simulation} has been finished"
  done
So I'll be very (very!!) thankful for possible suggestion regarding both
cases
Kind regards,
James
2014-09-26 11:43 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> Dear all,
>
> I wounder to ask some suggestions about possibility to improve my launch
> script aimed on the running of several similations.
>
> e.g my current protocol use simple looping over the dir with the
> simulations to run sh file in each folder which is call for the pmemd etc
> for each system
>
> #!/bin/bash
>
> # set workdir with proteins
> dirr=/home/gleb/Documents/script
> simulations=/home/gleb/Documents/script/Simulations
>
>
>
> #run each simulation
> for sim in $simulations/* ; do
>   simulation=$(basename "$sim")
>   echo "Simulation of ${simulation} is in a progress!"
>   cd $sim
>   chmod +x ./${simulation}.Sh
>   ./${simulation}.Sh
>   echo "Simulation of ${simulation} has been finished"
> done
>
> how this script can be improved to i) avoid call sh from the another sh?
> ii) to run several jobs in parallel corresponded to the number of available
> GPU of my workstation ?
>
> Thanks for help,
>
> James
>
------------------------------
Message: 10
Date: Fri, 26 Sep 2014 12:31:26 +0000
From: Parker de Waal <Parker.deWaal.vai.org>
Subject: Re: [AMBER] Combined cartesian and NMR restraints
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <974700F6B71AA04897B9105CC7E1AAFA7B3363.VAIEXMB01.vai.org>
Content-Type: text/plain; charset="us-ascii"
Another update - I've switched from CUDA 6.5 to 5.5, however the error remains the same:
Error: unspecified launch failure launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed unspecified launch failure
Is it possible that because both my cartesian restraints (only on chain A) AND NMR restraints (tethering chain B to chain A) affect some of the same residues that PMEMD.CUDA is crashing and that this combination is not possible?
Best,
Parker
________________________________________
From: Parker de Waal
Sent: Thursday, September 25, 2014 11:26 PM
To: AMBER Mailing List
Subject: RE: [AMBER] Combined cartesian and NMR restraints
Hi David,
Thank you for the input. I've adjusted the input per your suggestion as follows:
NVT prod
&cntrl
  irest=1, ntx =5,
  nstlim=5000000, dt=0.002,
  ntpr=500, ntwr=500, ntwx=500,
  temp0=300.0,
  ntt=3, gamma_ln=5, ntb=1, ntp=0,
  ntc=2, ntf=2, ig=-1,
  cut=9,
  ioutfm = 1,
  iwrap=1, nmropt=1,
  ntr=1, restraint_wt=20., restraintmask=':1-708',
/
&wt type='END' /
DISANG=rst.dist
The only problem now is that when I run pmemd.CUDA the follow error occurs:
Error: an illegal memory access was encountered launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered
I'm currently using the most recent version of AMBER14 (updated and recompiled today) with NVIDIA Driver Version: 340.32 and Cuda compilation tools, release 6.5, V6.5.12 (I'm running arch so rolling back is difficult, but I'm trying now to 5.5)
Parker
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Thursday, September 25, 2014 10:56 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Combined cartesian and NMR restraints
On Fri, Sep 26, 2014, Parker de Waal wrote:
>
> After reading through some of the old mailing list threads regarding
> the various workarounds for ntr =1 and nmropt=1, I still need some
> clarification.
>
> I have an NVT http://scanmail.trustwave.com/?c=129&d=49Wk1K_bbQBiQ3IZT3Q0OKQyeRAK9WcrWuJ7VB2iCg&u=http%3a%2f%2fprod%2ein as show below:
>
>
> Now I wish to add cartesian restraints, following the snippet here:
> http://scanmail.trustwave.com/?c=129&d=49Wk1K_bbQBiQ3IZT3Q0OKQyeRAK9WcrWuUuUBb1CQ&u=http%3a%2f%2fambermd%2eorg%2fQuestions%2fconstraints%2ehtml into my rst.dist file as
> seen below:
The group cards for cartesian restraints go into the mdin file, not into the
restraints file.
>
> #    N373 D69 VS
>  &rst
>   ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
>       rk2=0.0, rk3=25.0, ir6=1, ialtd=0,
>  &end
> ... (lines removed)
> #    A150 F244 VS
>  &rst
>   ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
>  &end
> Hold GPCR fixed
> 20.0
> RES 1 708
> END
> END
>
> However whenever I run this the follow error occurs:
>
>    5.  REFERENCE ATOM COORDINATES
>
>   default_name
>     ----- READING GROUP     1; TITLE:
>  DISANG=rst.dist
Note that the program thinks the DISANG card is the title for the cartesian
restraints; so somehow it is not reading the NMR-like restraints correctly.
The first thing you need to do is set ntr=0, and make sure that you are
getting the NMR restraints correctly processed.  Follow the example in the
$AMBERHOME/test/nmr directory.
By far the simplest thing to do for cartsian restraints is to set them
in the cntrl namelist:
   ntr=1, restraint_wt=20., restraintmask=':1-708',
Then there is no need for any GROUP input.
Beyond this:
You could try using the correct "/" rather than the obsolete (and never
standard "&end" to end namelists.  But that is probably not the source of the
problem.  You may need to let us know which program you are running
(sander or pmemd?) and which version.  Posting the entire mdout file is
probably also required...there is something subtle that is preventing your
file from being parsed correctly.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://scanmail.trustwave.com/?c=129&d=5NWk1DkJ-rwIWc9WjII5xYe7GxkTZDMTXvE-6uITXQ&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinfo%2famber
------------------------------
Message: 11
Date: Fri, 26 Sep 2014 20:49:17 +0800 (GMT+08:00)
From: ?? <shiw12.mails.tsinghua.edu.cn>
Subject: [AMBER] Fw: Welcome to Beijing for the 15th International
    Congress of Quantum Chemistry
To: amber <amber.ambermd.org>
Message-ID:
    <512ee358.8cd3.148b20223c9.Coremail.shiw12.mails.tsinghua.edu.cn>
Content-Type: text/plain; charset=UTF-8
Dear Colleagues,
The 15th International Congress of Quantum Chemistry (ICQC) will take place in Beijing, June 8-13, 2015. The registration will be opened by Oct 1, 2014. Please browse http://www.icqc2015.org/. The following eminent theoretical chemists have accepted the invitation for lectures:
Millard Alexander (U Maryland), Yuriko Aoki (Kyushu U), Paul Ayers (McMaster U), Joel Bowman (Emory U), Ria Broer-Braam (Groningen U), Filipp Furche (UC Irvine), Jiali Gao (U Minnesota), Yiqin Gao (Peking U), Stefan Grimme (U Bonn), Sharon Hammes-Schiffer (UIUC), Martin Head-Gordon (UC Berkeley), Dudley Herschbach (Harvard, Nobel Laureate), Roald Hoffmann (Cornell U, Nobel Laureate), Kendall Houk (UCLA), Denis Jacquemin (U Nantes), Poul J?rgensen (U Aarhus), Kwang S. Kim (Ulsan), Wanzhen Liang (Xiamen U), Carmay Lim (Acad Sinica), Yi Luo (KTH), Rudolf Marcus (Caltech, Nobel Laureate), Benedetta Mennucci (U Pisa), Josef Michl (U Colorado), Keiji Morokuma (U Kyoto), Hiroshi Nakatsuji (QCRI), Jozef Noga (Comenius U), Oleg Prezhdo (U So Calif), Leo Radom (U Sydney), Lucia Reining(Ecole Polytech), Andreas Savin (UPMC), George Schatz (Northwester U), H. Bernhard Schlegel (Wayne State U), Tamar Seideman (Northwestern U), Juha Vaara (U Oulu), Xin Xu (Fudan U),
 Yijing Yan (Hong Kong UST), Xueming Yang (DICP), Donghui Zhang (DICP)
The registration fee is 350 EUROs (regular) and 175 EUROs (student), which covers (i) conference and reception, coffee breaks, all the lunches; (ii) tour to the Great Wall; (iii)  refreshments in the four poster sessions.
The conference venue will be in the Tsinghua University Campus (ranked by Forbes as one of the 14 most beautiful University Campuses in the world, only one from Asia), easy connected by subways and other public transport. Many hotels, restaurants, supermarkets, cafes are within the distance of 20-minute walk. You may also easily rent a bicycle for one week or even one month for less than 10 EUROs. Beijing is a fantastic place to see. And this is the very first ICQC in China.
Please check the air quality of Beijing in  http://aqicn.org/city/beijing/ : Beijing is not much worse than other megacities like Tokyo or New York on average. The air quality in the first half of June will be satisfactory and it is sure that you will enjoy the sunshine and the cosy temperature.
There will be eight satellite meetings featuring on specialized directions of theoretical and computational chemistry. Please consult the website.
Please mark your calendar. We look forward to welcoming you in China!
Sincerely,
Zhigang Shuai, Weihai Fang, Wenjian Liu, Weitao Yang
Organizing Committee of the 15th ICQC
http://www.icqc2015.org/
------------------------------
Message: 12
Date: Fri, 26 Sep 2014 09:47:45 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] cpptraj/parmbox
To: amber.ambermd.org
Message-ID: <1411739265.29713.4.camel.gmail.com>
Content-Type: text/plain; charset="UTF-8"
On Fri, 2014-09-26 at 00:13 -0700, amirhossein taghavi wrote:
> Hello everyone,
> 
> My rpoblem is not directly related to MD but as I use Amber cpptraj to
> analyze my data, I wondered may some one could have some help!!
> 
> I have a CG model of DNA in xyz format and I am using cpptraj to do
> some measurements on bonds,angles and dihedrals.The problem is, for
> example, when I calculate the base interdistances with piece of a
> script I have, in some frames the distance is calculated with the
> image of particle at the end of the box, like say my box is 136A. so
> if the usual BB distance is between 5-7A is some frames it jumps tp
> 136.
> I have added parmbox information to the script but the problem still
> exists.
> any help or suggestion is highly appreciated.
By default, cpptraj uses the minimum image convention when computing
distances (unless you use the keyword "noimage").  If you are getting
wonky distances, perhaps your box is not correctly defined?
Your cpptraj output should provide information about your files (like,
for instance, any box information that may be present).  Does it look
right to you?
HTH,
Jason
-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 13
Date: Fri, 26 Sep 2014 07:59:59 -0600
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] cpptraj/parmbox
To: amirhossein taghavi <amirhosseintaghavi240.yahoo.com>,    AMBER
    Mailing List <amber.ambermd.org>
Message-ID:
    <CAAC0qOaO6Gd94+uQL6kshM1LhOiSiuY0DAP8ymUY+XnkzutiZA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
We need much more information on how the original trajectory was
generated, as well as the full cpptraj output to even begin to
diagnose this problem.
-Dan
On Fri, Sep 26, 2014 at 1:13 AM, amirhossein taghavi
<amirhosseintaghavi240.yahoo.com> wrote:
> Hello everyone,
>
> My rpoblem is not directly related to MD but as I use Amber cpptraj to analyze my data, I wondered may some one could have some help!!
>
> I have a CG model of DNA in xyz format and I am using cpptraj to do some measurements on bonds,angles and dihedrals.The problem is, for example, when I calculate the base interdistances with piece of a script I have, in some frames the distance is calculated with the image of particle at the end of the box, like say my box is 136A. so if the usual BB distance is between 5-7A is some frames it jumps tp 136.
> I have added parmbox information to the script but the problem still exists.
> any help or suggestion is highly appreciated.
>
> Thanks in Forward
> _______________________________________________
> 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: 14
Date: Fri, 26 Sep 2014 10:05:01 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Combined cartesian and NMR restraints
To: amber.ambermd.org
Message-ID: <1411740301.29713.6.camel.gmail.com>
Content-Type: text/plain; charset="UTF-8"
On Fri, 2014-09-26 at 12:31 +0000, Parker de Waal wrote:
> Another update - I've switched from CUDA 6.5 to 5.5, however the error remains the same:
> 
> Error: unspecified launch failure launching kernel kClearForces
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
> 
> Is it possible that because both my cartesian restraints (only on
> chain A) AND NMR restraints (tethering chain B to chain A) affect some
> of the same residues that PMEMD.CUDA is crashing and that this
> combination is not possible?
What happens if you turn off all of the restraints?  Does it work?
Does it work with the CPU?  Here is a good workflow for debugging
pmemd.cuda issues:
1. Run the pmemd.cuda test suite and make sure that the tests run, and
the majority pass (and that the failures are small differences). (This
should really be step 0, since hopefully you've already done this part.)
2. Does the pmemd.cuda simulation fail reliably?  That is, do you get
the EXACT same behavior every time? (i.e., it fails on the same step
with the same error message, and yields identical energies each time if
it gets that far?)
3a. If the answer to 2 is "no", download and run the GPU validation test
suite.  If that test fails, RMA your bad GPU and skip to step 6.  If the
test passes, continue to 3b or 4.
3b.  Try reducing the feature set of your simulation to make sure
"plain" molecular dynamics works.  If "plain" MD works, try adding the
"extras" separately until you find the minimal combination that fails.
This will help narrow down where to look.
4. Run the problematic simulation using pmemd on the CPU.  Does it fail?
5a. If it fails, have a look at the error message -- pmemd and pmemd.MPI
are very often better at giving informative error messages than
pmemd.cuda (which often just says the equivalent of "something went
wrong").
5b. If the CPU works, then the problem is more likely (although still
not certainly) a problem with pmemd.cuda, so consult this list, giving
as much detail as possible (including what you've done so far).
6. Have a beer.  Or a glass of milk.
Of course there are more things you can try -- like reducing ntpr and
ntwx to very small numbers (e.g., 1) so that you can visualize what is
happening each step leading up to the crash (you may have to run some MD
to get your system "close" if it happens after thousands of steps).
Hope this helps,
Jason
-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 15
Date: Fri, 26 Sep 2014 17:21:04 +0200
From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Subject: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
    <CACF5EqmCBhLNGjw978r50tFrxrT5rVrUVw7GX=j7NkpfsiQg3A.mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Amberists;
I am running tleap using AMBER 12 with the following script on a receptor
which is attached herewith. During running the Leap I am encountering this
problem
"
FATAL:  Atom .R<NLEU -1>.A<H 22> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Writing pdb file: rec_solvated.pdb
Converting N-terminal residue name to PDB format: NLEU -> LEU
Converting C-terminal residue name to PDB format: CLEU -> LEU
Quit
"
I would highly appreciate any response in this regard.
Thank you for all your time.
tleap.in
source leaprc.ff99SB
receptor = loadPDB rec.pdb
saveAmberParm receptor rec.top rec.crd
charge receptor
addIons2 receptor Cl- 0
solvateBox receptor TIP3PBOX 8.0
saveAmberParm receptor rec_solvated.top rec_solvated.crd
savepdb receptor rec_solvated.pdb
quit
-- 
Thanks & Regards;
Soumendranath Bhakat
Researcher
Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
Past: Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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------------------------------
Message: 16
Date: Fri, 26 Sep 2014 11:26:22 -0400
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a
    type
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
    <CAGk3s-QCFhE6dJNH=A=mxmLk08RCQDVBCXuJe7XQ_iKYqYeQ6A.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
if you look at your PDB file, you'll see that there are H atoms listed only
for NLEU, not for any other residue. also, these H atoms all have the same
name. Perhaps you might want to look into the source of this pdb file, and
see if those H atoms really should be in your file or not. If so, you need
to tell Amber which atom each of these H's are, since it doesnt' really
have a way to figure it out if the names are all just "H".
On Fri, Sep 26, 2014 at 11:21 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Dear Amberists;
>
> I am running tleap using AMBER 12 with the following script on a receptor
> which is attached herewith. During running the Leap I am encountering this
> problem
>
> "
> FATAL:  Atom .R<NLEU -1>.A<H 22> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Writing pdb file: rec_solvated.pdb
>  Converting N-terminal residue name to PDB format: NLEU -> LEU
>  Converting C-terminal residue name to PDB format: CLEU -> LEU
> Quit
> "
>
> I would highly appreciate any response in this regard.
> Thank you for all your time.
>
>
> tleap.in
>
> source leaprc.ff99SB
> receptor = loadPDB rec.pdb
> saveAmberParm receptor rec.top rec.crd
> charge receptor
> addIons2 receptor Cl- 0
> solvateBox receptor TIP3PBOX 8.0
> saveAmberParm receptor rec_solvated.top rec_solvated.crd
> savepdb receptor rec_solvated.pdb
> quit
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
> Researcher
> Molecular Modelling and Drug Design Research Group
> Discipline of Pharmaceutical Sciences
> UKZN, Westville
> Weblink: http://soliman.ukzn.ac.za/Home.aspx
> Past: Department of Pharmaceutical Sciences
> Birla Institute of Technology, Mesra, India
> in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
------------------------------
Message: 17
Date: Fri, 26 Sep 2014 11:54:02 -0400
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a
    type
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20140926155402.GB3761.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Fri, Sep 26, 2014, Soumendranath Bhakat wrote:
> FATAL:  Atom .R<NLEU -1>.A<H 22> does not have a type.
To expand/simplify what Carlos said:
Your PDB file has a atom named "H" in the first resdidue.  But the
IUPAC/PDB/Amber nomenclature for an N-terminal amino acid does not have any
such atoms: the three hydrogens bonded to the "N" atom are called H1, H2, and
H3.
So, the PDB atom names don't match the library atom names, and tleap doesn't
know what to do, and quits.
As Carlos said, the simplest thing to do is just to remove the "H" atom
from the PDB file.  Another option is to use the "reduce" program first.
Even better would be to get in the habit of using "pdb4amber" before running
tleap.
...dac
------------------------------
Message: 18
Date: Fri, 26 Sep 2014 08:57:15 -0700
From: Ross Walker <ross.rosswalker.co.uk>
Subject: Re: [AMBER] bash scripting for MD tasks
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <D04AD9B9.49AC4%ross.rosswalker.co.uk>
Content-Type: text/plain;    charset="US-ASCII"
Hi James,
I haven't looked through the syntax here completely but one thing to note:
On 9/26/14, 4:14 AM, "James Starlight" <jmsstarlight.gmail.com> wrote:
>The general idea here to avoid palatalization and just run jobs still
>being
>in loop using 2 variables one corresponded to the looping over GPUs iDs
>and
>the second to the folder of each simulation.
>Below you could find two examples (unfortunately both still incomplete
>because I'm not an expert in BASH)
>
>#!/bin/bash
>
># set workdir with proteins
>dirr=/home/gleb/Documents/script
>simulations=/home/gleb/Documents/script/Simulations
>
>#run each simulation in parallel using nested loop which might not be good
>solution : here the problem that some condition should be provided to
>avoid
>using >1 simulation on the same GPU
>#
>i=0 # the number of first GPU which will be used!
>while i < n ; do # the maximum number of the available GPUs on the
>machines
># m.b n also might be obtained using some command ?
> # !!!!some condition should be specified to pass sharing SAME GPU between
>different md runs !!!
> export CUDA_VISIBLE_DEVICES "$i"
> for sim in $simulations/* ; do
>   simulation=$(basename "$sim")
>   echo "Simulation of ${simulation} is in a progress on ${i} GPU!!"
>   cd $sim
>   chmod +x ./${simulation}.Sh
>  ./${simulation}.Sh &
---> without a 'wait' here the echo line below will immediately be printed
because you backgrounded the previous command. The better way to do this
is to put the GPU loop as the inner loop and the simulations as the outer
loop. And include a 'wait' after the done on the inner loop. This will
work reasonably efficiently as long as the simulations take similar wall
clock times. The alternative is to have an actual fork in your bash script
- run it in multiple threads or using 'parallel' - I forget the syntax. Or
alternatively run two completely separate bash scripts, or install a
queuing system.
Note if you set the GPUs to exclusive process mode (nvidia-smi -c 3) then
you do not need to set CUDA_VISIBLE_DEVICES. pmemd.cuda will automatically
select a free GPU. However this will disable multiGPU runs using peer to
peer so you need to set it back to default (nvidia-smi -c 0) if you want
to run pmemd.cuda.MPI.
>   echo "Simulation of ${simulation} has been finished"
>  done
>done
HTH,
All the best
Ross
>
------------------------------
Message: 19
Date: Fri, 26 Sep 2014 11:21:42 -0600
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] cpptraj/parmbox
To: amirhossein taghavi <amirhosseintaghavi240.yahoo.com>,    AMBER
    Mailing List <amber.ambermd.org>
Message-ID:
    <CAAC0qOb3tey5JLtNyggTZR8pMxHsc=Ej7kr0Zb0QToZRCyaG4A.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
You've come across a corner case. The problem is that since the
trajectory only contains box lengths (no angles), cpptraj by default
checks the topology to determine what kind of box is present. However,
since you are presumably using your PDB file as your topology (which
has no box info), cpptraj doesn't know what kind of box it is. In the
end the coordinates are read in fine, but the box information is not
used because cpptraj doesn't assume the box is orthogonal.
The 'parmbox' command can help, but since you only gave it lengths
(not angles) it still has no idea what the box type is. Add 'alpha 90
beta 90 gamma 90' to the 'parmbox' command to set an orthogonal box.
Hope this helps,
-Dan
On Fri, Sep 26, 2014 at 8:19 AM, amirhossein taghavi
<amirhosseintaghavi240.yahoo.com> wrote:
> Hi,
>
> The original trajectory file is the output of my MC code for GC DNA modeling
> in the xyz format.I have two scripts which produce pdb and trj files which
> based on that cpptraj analysis is done.
>
> This is a sample of cpptraj output:
>
> Reading '1.xyz.pdb' as PDB File
>     1.xyz.pdb: determining bond info from distances.
> Warning: 1.xyz.pdb: Determining default bond distances from element types.
> INPUT: Reading Input from STDIN
>   [parmbox x 136.12 y 136.12 z 136.12]
>   [trajin 1.xyz.trj]
>     Reading '1.xyz.trj' as Amber Trajectory
>   [distance .82 @82 out distBB_41.dat geom noimage]
>     DISTANCE: .82 to @82, non-imaged, geometric center.
>
> I have attached the original trajectory file and trj,pdb files hope that it
> helps.if the scripts that are used to get pdb and trj files are also needed
> please let me know.
>
> Thanks in Forward
> Amir
>
>
>
>
> On Friday, September 26, 2014 4:00 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>
> Hi,
>
> We need much more information on how the original trajectory was
> generated, as well as the full cpptraj output to even begin to
> diagnose this problem.
>
> -Dan
>
> On Fri, Sep 26, 2014 at 1:13 AM, amirhossein taghavi
> <amirhosseintaghavi240.yahoo.com> wrote:
>> Hello everyone,
>>
>> My rpoblem is not directly related to MD but as I use Amber cpptraj to
>> analyze my data, I wondered may some one could have some help!!
>>
>> I have a CG model of DNA in xyz format and I am using cpptraj to do some
>> measurements on bonds,angles and dihedrals.The problem is, for example, when
>> I calculate the base interdistances with piece of a script I have, in some
>> frames the distance is calculated with the image of particle at the end of
>> the box, like say my box is 136A. so if the usual BB distance is between
>> 5-7A is some frames it jumps tp 136.
>> I have added parmbox information to the script but the problem still
>> exists.
>> any help or suggestion is highly appreciated.
>>
>> Thanks in Forward
>
>> _______________________________________________
>> 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)
>
-- 
-------------------------
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)
------------------------------
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Received on Mon Sep 29 2014 - 01:00:02 PDT
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