date:20121126


Hello:

 I found that someone mentioned that there is a script from Mark which 
could be used to convert CGenff format into Gromacs .itp file. I 
searched the mailist and didn't find it.

  I am just wondering where can I obtain this script?

thank you very much
best
Albert
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[gmx-users] Re: energy-mimisation-problem

2012-11-26 Thread SANTU BISWAS

On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS santu.biswa...@gmail.com wrote:
 dear users,

When performing a energy minimization of a
 polypeptide(formed by lysine-5-residues) in vacuum box by using
 Steepest Descent and also Conjugate Gradient methods in gromacs double
 precision,i noted that GROMACS never converges to emtol values under
 about 0.1 kj/mol/nm.I have used the .mdp file which is given below



 title=
 cpp  = /lib/cpp
 ;include  =-I../top/
 define   = -DFLEXIBLE

 ; RUN CONTROL PARAMETERS =
 integrator   = steep
 ; start time and timestep in ps =
 tinit= 0
 dt   = 0.001
 nsteps   = 1000
 rlist= 0.9
 rcoulomb = 0.9
 ; Method for doing Van der Waals
 vdw-type = Cut-off
 ; cut-off lengths
 rvdw_switch  = 0
 rvdw = 0.9
 ; Neighbour searching
 nstlist  = 1
 ; ENERGY MINIMIZATION OPTIONS =
 emtol= 0.1
 emstep   = 0.1
 nstcgsteep   = 1000




 santu
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Re: [gmx-users] where is the script?

2012-11-26 Thread David van der Spoel


On 2012-11-26 12:00, Albert wrote:

Hello:

  I found that someone mentioned that there is a script from Mark which
could be used to convert CGenff format into Gromacs .itp file. I
searched the mailist and didn't find it.
   I am just wondering where can I obtain this script?

thank you very much
best
Albert

It's posted on the website.

http://www.gromacs.org/Downloads/User_contributions/Other_software
You want this one:  charmm2gromacs-pvm.py

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Re: force vs time plot

2012-11-26 Thread Thomas Schlesier


This should be in the pullf.xvg (time and then the forces).



Am 24.11.2012 19:55, schrieb gmx-users-requ...@gromacs.org:

Hi to all gromacs users,

I am trying to run an umbrella sampling and i am getting the initial 
conformations by pulling simulations but i want to check the simulation through 
the force vs time plot to see if my complex did or did not separate, so how can 
i get this plot?

Thank you for your time

Paula


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Re: [gmx-users] GPU warnings

2012-11-26 Thread Szilárd Páll

On Sun, Nov 25, 2012 at 8:47 PM, Thomas Evangelidis teva...@gmail.comwrote:

 Hi Szilárd,

 I was able to run code compiled with icc 13 on Fedora 17, but as I don't
  have Intel Compiler v13 on this machine I can't check it now.
 
  Please check if it works for you with gcc 4.7.2 (which is the default)
 and
  let me know if you succeed. The performance difference between icc and
 gcc
  on your processor should be negligible with GPU runs and at most 5-10%
 with
  CPU-only runs.
 
  As the issue is quite annoying, I'll try to have a look later, probably
  after the beta is out.
 
 
 gcc 4.7.2 is not supported by any CUDA version.


I suggest that you just fix it by editing the include/host_config.h and
changing the version check macro (line 82 AFAIK). I've never had real
problems with using new and officially not supported gcc-s, the version
check is more of a promise from NVIDIA that we've tested thoroughly
internally and we more or less vouch for thins combination.

Cheers,
--
Szilárd

PS:
Disclamer: I don't take responsibility if your machine goes up in flames! ;)



 Thomas
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Re: [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5

2012-11-26 Thread Szilárd Páll

Or run any binary with the -version option e.g:
$ mdrun -version

--
Szilárd


On Sun, Nov 25, 2012 at 10:30 AM, Mark Abraham mark.j.abra...@gmail.comwrote:

 Look at the top of the output of any GROMACS program.

 Mark

 On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett acootbr...@yahoo.com
 wrote:

  Dear All,
 
  Is any gromacs command which can tell us or distinguish whether what
  installed is gromacs 4.5.4 or 4.5.5?
 
  Cheers,
 
  Acoot
 
 
  --- On Sat, 24/11/12, David van der Spoel sp...@xray.bmc.uu.se wrote:
 
   From: David van der Spoel sp...@xray.bmc.uu.se
   Subject: Re: [gmx-users] Different average H bonds with different
  g_hbond releases
   To: Discussion list for GROMACS users gmx-users@gromacs.org
   Received: Saturday, 24 November, 2012, 5:30 PM
   On 2012-11-24 05:41, Acoot Brett
   wrote:
If we got the results by 4.5.4, what will be the method
   to analyze it by 4.5.5? By a pathch or by installation of
   4.5.5 to analyze the 4.5.4 results?
   
   In practice there is no problem to have a number of gromacs
   versions
   installed. It is typically not recommended to switch gromacs
   versions of
   mdrun during a project - unless there are know issues
   -  but for the
   analysis this is less critical. In this case 4.5.5 should be
   used.
  
Cheers,
   
Acoot
   
--- On Sat, 24/11/12, Justin Lemkul jalem...@vt.edu
   wrote:
   
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Different average H bonds
   with different g_hbond releases
To: Discussion list for GROMACS users gmx-users@gromacs.org
Received: Saturday, 24 November, 2012, 9:30 AM
   
   
On 11/23/12 5:23 PM, Luigi CAVALLO wrote:
   
   
Hi,
   
we have a .xtc and .tpr file. We were
   interested in
the
average number of H-bonds in the last 10ns of a
   60ns
long trajectory. We
analyzed the jobs as g_hbond -f
   traj1_0-60ns.xtc -s
topol.tpr -b 5
-num hbond.xvg. We are displaced by having a
   different
number depending
on the g_hbond release.
   
Release 4.5.4 : Average number of hbonds per
timeframe 163.620 out of 118112 possible
   
Release 4.5.5 : Average
number of hbonds per timeframe 168.168 out of
   118112
possible
   
Looking
at the hbond.xvg file, the number of H-bonds in
   each
frame are clearly
different between the two releases. How is
   this
possible ? We checked
single versus double precision g_hbonds, same
   behavior.
We checked that
the initial part of the output, i.e. all the
   various
g_hbond defaults,
they are the same. We tested different
   computers and
compilations, same
behavior.
   
The topology and the md run were done with
   release
4.5.4 if
this could be a relevant information.
   
   
There was a bug that was fixed in May 2011 wherein
   4.5.4
reported too few
hydrogen bonds.
   
commit 91a481fad7ef0d87a4f8b2cb633c9dc40644350c
Author: Erik Marklund er...@anfinsen.bmc.uu.se
Date:   Tue May 10 14:37:10 2011
   +0200
   
  Fixed long standing
   bug where the
merging resulted in too few hbonds.
   
   
-Justin
   
--

   
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
   

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   --
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   Dept. of Cell  Molec. Biol., Uppsala University.
   Box 596, 75124 Uppsala, Sweden. Phone:
   +46184714205.
   sp...@xray.bmc.uu.se
 http://folding.bmc.uu.se
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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0




On 11/26/12 12:58 AM, Venkat Reddy wrote:

Dear all,
I am simulating a Protein-Drug complex. I am following Justin's tutorial. I
have used *PRODRG *for generating topology. *Gaussian *has given me the ESP
charges. I have edited the charges in the itp file using the *Gaussian*'s
ESP charges*. *Then I am getting this strange error.

  *ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*



Probably there are some hidden line ending problems.  Did you edit the file with 
a plain text editor?


Also note...


 24   CH2 1  ORP  C5 40.354  13.0190
 *25   CH1 1  ORP  C4 4   -0.024  14.0270*


These masses don't make sense.  CH2 should have a mass of 14.027 and CH1 should 
have a mass of 13.019.  I've never seen PRODRG get something like this wrong; 
were you sure to carefully change the file?  It seems something has gone very 
wrong here.


Compare the original topology (from PRODRG) with the one you edited.  If grompp 
succeeds using the PRODRG topology (stop using it after that point), then the 
error arose due to something you did when editing the file.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: energy-mimisation-problem




On 11/26/12 6:01 AM, SANTU BISWAS wrote:

On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS santu.biswa...@gmail.com wrote:

dear users,

When performing a energy minimization of a
polypeptide(formed by lysine-5-residues) in vacuum box by using
Steepest Descent and also Conjugate Gradient methods in gromacs double
precision,i noted that GROMACS never converges to emtol values under
about 0.1 kj/mol/nm.I have used the .mdp file which is given below



title=
cpp  = /lib/cpp
;include  =-I../top/
define   = -DFLEXIBLE

; RUN CONTROL PARAMETERS =
integrator   = steep
; start time and timestep in ps =
tinit= 0
dt   = 0.001
nsteps   = 1000
rlist= 0.9
rcoulomb = 0.9
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw_switch  = 0
rvdw = 0.9
; Neighbour searching
nstlist  = 1
; ENERGY MINIMIZATION OPTIONS =
emtol= 0.1
emstep   = 0.1
nstcgsteep   = 1000



Are you using single or double precision?  Single precision steepest descents is 
unlikely to ever reach such a low emtol.  Double precision and more thorough 
methods (CG and/or L-BFGS) may achieve it, perhaps after several rounds of each.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Umbrella sampling - regd




On 11/26/12 1:03 AM, ramesh cheerla wrote:

Dear Gromacs users,


  I am calculating  PMF for the ion permeation through a tunnel, using
umbrella sampling. In my system I have some binding sites with ions, I have
removed some ions from binding sites before pulling and In pulling
simulations have pullaed pulled the adjacent ions to the vacant binding
site (tunnel is aligned along  Y- axis).
for this I have used the following options in .mdp file.
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N Y N
pull_start  = yes
pull_ngroups= 1
pull_group0 = REFA
pull_rate1  = 0.01
pull_k1 = 3000  ; kJ mol^-1 nm^-2

Here  pull_group0 = REFA is the ion at another binding site and
pull_group1 = ATBP  is the atom  that I am pulling to the vacant site.
In next step I have performed umbrella sampling simulations to the selected
configurations using the following options :
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N Y N
pull_start  = yes   ; define initial COM distance  0
pull_ngroups= 1
pull_group0 = REFA
pull_group1 = ATBP
pull_init1  = 0
pull_rate1  = 0.0  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 3000  ; kJ mol^-1 nm^-2
pull_nstxout= 100
pull_nstfout= 100
After that I have constructed PMF profile using Gromacs tool g_wham,
while using g_wham I am getting the following warnings,
WARNING, no data point in bin 34 (z=0.889382) !
You may not get a reasonable profile. Check your histograms!
I have checked my histograms instead of one histogram for each
configuration with perfect overlapping, I am getting only one histogram.


You're probably just plotting the file wrong.

xmgrace -nxy histo.xvg


Here I am sending the link that containing PMF profile and histogram that
have obtained.
http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg
http://researchweb.iiit.ac.in/~bipin.singh/hist.jpg



The PMF suggests massive undersampling (or complete lack of sampling) in several 
areas.



the weired thing that I have observed in my pulling simulations is that I
have expected motion of ion in positive Y-direction for my pull parameters
but it is moving in negative Y- direction.
  Can anybody please suggest me a solution for this,  Am I following correct
protocol to get PMF of my system, is there any better method that suits for
my system.



If you are trying to see a complete translocation of an ion through a channel, 
the distance geometry is inappropriate, as it does not deal correctly with the 
change of sign for the vector between the reference and pulled group, IIRC.  Try 
position geometry and associated settings.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] where is the script?


On 11/26/2012 02:36 PM, David van der Spoel wrote:

It's posted on the website.

http://www.gromacs.org/Downloads/User_contributions/Other_software
You want this one:charmm2gromacs-pvm.py

--


thanks a lot for kind reply.

But how to use it? I am trying to run with command:


python charmm2gromacs-pvm.py charmm.rtf

but it said:


Traceback (most recent call last):
  File charmm2gromacs-pvm.py, line 33, in module
parFile = open(sys.argv[2], 'r')
IndexError: list index out of range



I open the script, it said:

inparameters:
command line parameters:
1charmm topology file
2corresponding charmm parameter file
3optfoldername, default cgenff.ff

outfiles:
1foldername/atomtypes.atp
2foldername/forcefield.itp
3foldername/forcefield.doc
4foldername/aminoacids.rtp
5foldername/ffbonded.itp
6foldername/ffnonbonded.itp
7foldername/forcefield.r2b
8optfoldername/lipids.rtp(if '!lipid 
section' statement in CHARMM top file)

9optfoldername/cmap.itp(if genCMAP = True)


It seems that the input file is a folder instead of a single file? I 
generate my ligand topology from the CGenFF website and I only get a 
.rst file


THX

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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
gedit in linux.


On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/26/12 12:58 AM, Venkat Reddy wrote:

 Dear all,
 I am simulating a Protein-Drug complex. I am following Justin's tutorial.
 I
 have used *PRODRG *for generating topology. *Gaussian *has given me the
 ESP
 charges. I have edited the charges in the itp file using the *Gaussian*'s
 ESP charges*. *Then I am getting this strange error.

   *ERROR 1 [file protein.top, line 75]:*
 *  atom C4 (Res ORP-1) has mass 0*
 *
 *
 *
 *
 *
 *
 *ERROR 2 [file protein.top, line 75]:*
 *  atom C14 (Res ORP-1) has mass 0*


 Probably there are some hidden line ending problems.  Did you edit the
 file with a plain text editor?

 Also note...

   24   CH2 1  ORP  C5 40.354  13.0190
  *25   CH1 1  ORP  C4 4   -0.024  14.0270*


 These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
 should have a mass of 13.019.  I've never seen PRODRG get something like
 this wrong; were you sure to carefully change the file?  It seems something
 has gone very wrong here.

 Compare the original topology (from PRODRG) with the one you edited.  If
 grompp succeeds using the PRODRG topology (stop using it after that point),
 then the error arose due to something you did when editing the file.

 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0




On 11/26/12 9:12 AM, Venkat Reddy wrote:

Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
gedit in linux.



Regardless, the masses I pointed out are wrong.  You should still do the test to 
#include the original topology and see if it works, then if it does, figure out 
the source of the error in your file.


-Justin



On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/26/12 12:58 AM, Venkat Reddy wrote:


Dear all,
I am simulating a Protein-Drug complex. I am following Justin's tutorial.
I
have used *PRODRG *for generating topology. *Gaussian *has given me the
ESP
charges. I have edited the charges in the itp file using the *Gaussian*'s
ESP charges*. *Then I am getting this strange error.

   *ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*



Probably there are some hidden line ending problems.  Did you edit the
file with a plain text editor?

Also note...

   24   CH2 1  ORP  C5 40.354  13.0190

  *25   CH1 1  ORP  C4 4   -0.024  14.0270*



These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
should have a mass of 13.019.  I've never seen PRODRG get something like
this wrong; were you sure to carefully change the file?  It seems something
has gone very wrong here.

Compare the original topology (from PRODRG) with the one you edited.  If
grompp succeeds using the PRODRG topology (stop using it after that point),
then the error arose due to something you did when editing the file.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Thanks Justin...I will certainly do.


On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/26/12 9:12 AM, Venkat Reddy wrote:

 Dear Justin,
 I haven't touched the *Mass column.* I have edited the charges only using
 gedit in linux.


 Regardless, the masses I pointed out are wrong.  You should still do the
 test to #include the original topology and see if it works, then if it
 does, figure out the source of the error in your file.

 -Justin


 On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/26/12 12:58 AM, Venkat Reddy wrote:

  Dear all,
 I am simulating a Protein-Drug complex. I am following Justin's
 tutorial.
 I
 have used *PRODRG *for generating topology. *Gaussian *has given me the
 ESP
 charges. I have edited the charges in the itp file using the
 *Gaussian*'s
 ESP charges*. *Then I am getting this strange error.

*ERROR 1 [file protein.top, line 75]:*
 *  atom C4 (Res ORP-1) has mass 0*
 *
 *
 *
 *
 *
 *
 *ERROR 2 [file protein.top, line 75]:*
 *  atom C14 (Res ORP-1) has mass 0*


  Probably there are some hidden line ending problems.  Did you edit the
 file with a plain text editor?

 Also note...

24   CH2 1  ORP  C5 40.354  13.0190

   *25   CH1 1  ORP  C4 4   -0.024  14.0270*


 These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
 should have a mass of 13.019.  I've never seen PRODRG get something like
 this wrong; were you sure to carefully change the file?  It seems
 something
 has gone very wrong here.

 Compare the original topology (from PRODRG) with the one you edited.  If
 grompp succeeds using the PRODRG topology (stop using it after that
 point),
 then the error arose due to something you did when editing the file.

 -Justin

 --
 ====


 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
 h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 

 ====

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 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Dear Justin,
One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?


On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/26/12 9:12 AM, Venkat Reddy wrote:

 Dear Justin,
 I haven't touched the *Mass column.* I have edited the charges only using
 gedit in linux.


 Regardless, the masses I pointed out are wrong.  You should still do the
 test to #include the original topology and see if it works, then if it
 does, figure out the source of the error in your file.

 -Justin


 On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/26/12 12:58 AM, Venkat Reddy wrote:

  Dear all,
 I am simulating a Protein-Drug complex. I am following Justin's
 tutorial.
 I
 have used *PRODRG *for generating topology. *Gaussian *has given me the
 ESP
 charges. I have edited the charges in the itp file using the
 *Gaussian*'s
 ESP charges*. *Then I am getting this strange error.

*ERROR 1 [file protein.top, line 75]:*
 *  atom C4 (Res ORP-1) has mass 0*
 *
 *
 *
 *
 *
 *
 *ERROR 2 [file protein.top, line 75]:*
 *  atom C14 (Res ORP-1) has mass 0*


  Probably there are some hidden line ending problems.  Did you edit the
 file with a plain text editor?

 Also note...

24   CH2 1  ORP  C5 40.354  13.0190

   *25   CH1 1  ORP  C4 4   -0.024  14.0270*


 These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
 should have a mass of 13.019.  I've never seen PRODRG get something like
 this wrong; were you sure to carefully change the file?  It seems
 something
 has gone very wrong here.

 Compare the original topology (from PRODRG) with the one you edited.  If
 grompp succeeds using the PRODRG topology (stop using it after that
 point),
 then the error arose due to something you did when editing the file.

 -Justin

 --
 ====


 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
 h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 

 ====

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 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0




On 11/26/12 9:35 AM, Venkat Reddy wrote:

Dear Justin,
One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?




PRODRG doesn't even do a very good job of being compatible with 43A1, so if you 
re-derive the charges correctly, the result is compatible with 53A6.  PRODRG 
basically just uses 43A1 atom types, the names of which are largely the same in 
53A6, even if the parameters are slightly different, and thus I view PRODRG as a 
method to create generic Gromos96 topologies, given that the user has to do a 
fair amount of work to create a usable topology anyway.


-Justin


On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/26/12 9:12 AM, Venkat Reddy wrote:


Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
gedit in linux.



Regardless, the masses I pointed out are wrong.  You should still do the
test to #include the original topology and see if it works, then if it
does, figure out the source of the error in your file.

-Justin



On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/26/12 12:58 AM, Venkat Reddy wrote:

  Dear all,

I am simulating a Protein-Drug complex. I am following Justin's
tutorial.
I
have used *PRODRG *for generating topology. *Gaussian *has given me the
ESP
charges. I have edited the charges in the itp file using the
*Gaussian*'s
ESP charges*. *Then I am getting this strange error.

*ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*


  Probably there are some hidden line ending problems.  Did you edit the

file with a plain text editor?

Also note...

24   CH2 1  ORP  C5 40.354  13.0190


   *25   CH1 1  ORP  C4 4   -0.024  14.0270*



These masses don't make sense.  CH2 should have a mass of 14.027 and CH1
should have a mass of 13.019.  I've never seen PRODRG get something like
this wrong; were you sure to carefully change the file?  It seems
something
has gone very wrong here.

Compare the original topology (from PRODRG) with the one you edited.  If
grompp succeeds using the PRODRG topology (stop using it after that
point),
then the error arose due to something you did when editing the file.

-Justin

--
====


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




====

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--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Thank yo Justin for your help...I have generated the same topology using *ATB.
*Now, I got the masses correctly (as pointed out by you). So, I'm afraid
that is there any bug in PRODRG server?


On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/26/12 9:35 AM, Venkat Reddy wrote:

 Dear Justin,

 One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
 topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
 mix 53A6 and 43A1?



 PRODRG doesn't even do a very good job of being compatible with 43A1, so
 if you re-derive the charges correctly, the result is compatible with 53A6.
  PRODRG basically just uses 43A1 atom types, the names of which are largely
 the same in 53A6, even if the parameters are slightly different, and thus I
 view PRODRG as a method to create generic Gromos96 topologies, given that
 the user has to do a fair amount of work to create a usable topology anyway.

 -Justin

  On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/26/12 9:12 AM, Venkat Reddy wrote:

  Dear Justin,
 I haven't touched the *Mass column.* I have edited the charges only
 using
 gedit in linux.


  Regardless, the masses I pointed out are wrong.  You should still do
 the
 test to #include the original topology and see if it works, then if it
 does, figure out the source of the error in your file.

 -Justin


  On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/26/12 12:58 AM, Venkat Reddy wrote:

   Dear all,

 I am simulating a Protein-Drug complex. I am following Justin's
 tutorial.
 I
 have used *PRODRG *for generating topology. *Gaussian *has given me
 the
 ESP
 charges. I have edited the charges in the itp file using the
 *Gaussian*'s
 ESP charges*. *Then I am getting this strange error.

 *ERROR 1 [file protein.top, line 75]:*
 *  atom C4 (Res ORP-1) has mass 0*
 *
 *
 *
 *
 *
 *
 *ERROR 2 [file protein.top, line 75]:*
 *  atom C14 (Res ORP-1) has mass 0*


   Probably there are some hidden line ending problems.  Did you edit
 the

 file with a plain text editor?

 Also note...

 24   CH2 1  ORP  C5 40.354  13.0190

 *25   CH1 1  ORP  C4 4   -0.024  14.0270*


  These masses don't make sense.  CH2 should have a mass of 14.027 and
 CH1
 should have a mass of 13.019.  I've never seen PRODRG get something
 like
 this wrong; were you sure to carefully change the file?  It seems
 something
 has gone very wrong here.

 Compare the original topology (from PRODRG) with the one you edited.
  If
 grompp succeeds using the PRODRG topology (stop using it after that
 point),
 then the error arose due to something you did when editing the file.

 -Justin

 --
 ==**==



 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin**
 http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin
 
 h**ttp://www.bevanlab.**biochem.vt.**edu/Pages/**Personal/justin
 http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 



 ==**==


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  --
 ====

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin

Re: [gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0




On 11/26/12 9:43 AM, Venkat Reddy wrote:

Thank yo Justin for your help...I have generated the same topology using *ATB.
*Now, I got the masses correctly (as pointed out by you). So, I'm afraid
that is there any bug in PRODRG server?




I have no idea.  I haven't used PRODRG in a very long time.

-Justin


On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/26/12 9:35 AM, Venkat Reddy wrote:


Dear Justin,

One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?




PRODRG doesn't even do a very good job of being compatible with 43A1, so
if you re-derive the charges correctly, the result is compatible with 53A6.
  PRODRG basically just uses 43A1 atom types, the names of which are largely
the same in 53A6, even if the parameters are slightly different, and thus I
view PRODRG as a method to create generic Gromos96 topologies, given that
the user has to do a fair amount of work to create a usable topology anyway.

-Justin

  On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul jalem...@vt.edu wrote:





On 11/26/12 9:12 AM, Venkat Reddy wrote:

  Dear Justin,

I haven't touched the *Mass column.* I have edited the charges only
using
gedit in linux.


  Regardless, the masses I pointed out are wrong.  You should still do

the
test to #include the original topology and see if it works, then if it
does, figure out the source of the error in your file.

-Justin


  On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote:





On 11/26/12 12:58 AM, Venkat Reddy wrote:

   Dear all,


I am simulating a Protein-Drug complex. I am following Justin's
tutorial.
I
have used *PRODRG *for generating topology. *Gaussian *has given me
the
ESP
charges. I have edited the charges in the itp file using the
*Gaussian*'s
ESP charges*. *Then I am getting this strange error.

 *ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
*
*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*


   Probably there are some hidden line ending problems.  Did you edit
the


file with a plain text editor?

Also note...

 24   CH2 1  ORP  C5 40.354  13.0190

 *25   CH1 1  ORP  C4 4   -0.024  14.0270*



  These masses don't make sense.  CH2 should have a mass of 14.027 and

CH1
should have a mass of 13.019.  I've never seen PRODRG get something
like
this wrong; were you sure to carefully change the file?  It seems
something
has gone very wrong here.

Compare the original topology (from PRODRG) with the one you edited.
  If
grompp succeeds using the PRODRG topology (stop using it after that
point),
then the error arose due to something you did when editing the file.

-Justin

--
==**==



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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin**
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Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

[gmx-users] maxwell-boltzmann distribution

2012-11-26 Thread Zahra M

Hi dear GROMACS experts

I wanna know if GROMACS uses only Maxwell-Boltzmann distribution
in statistical mechanics, or it also uses Fermi-Dirac and Bose-Einstein 
statistics.If it only uses Maxwell-Boltzmann distribution, are the results 
reliable and correct? I mean can we use this law, which is based on the Kinetic 
Theory of Gases, for a system containing protein (that is not in gaseous 
state)? If we can use it, why?
 
Bests
-Zahra

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[gmx-users] Installation problems with MacOS 10.7.5

2012-11-26 Thread Stefan Jasconek


Dear Users,
I have problems with the installation of GROMACS 4.5.5 on MacOS 10.7.5.
GCC version 4.2.1
FFTW is: FFTW-3.3.2.
The CMAke command
cmake -DGMX_THREAD_MPI=OFF \
   -DFFTW3F_INCLUDE_DIR=$FFTWDIR/include \
   -DFFTW3F_LIBRARIES=$FFTWDIR/lib \
   -DGMX_X11=OFF \
   -DCMAKE_INSTALL_PREFIX=$(pwd) \
   -DGMX_MPI=OFF \
   -DGMX_THREADS=OFF \
   -DBUILD_SHARED_LIBS=OFF \
/Users/jaschone/Downloads/gromacs-4.5.5
Where CCDIR is the location of the GCC binary, FFTWDIR is the location 
of the FFTW stuff.


I get the following error mesage:
WARNING: Target md requests linking to directory 
/Users/jaschone/progs/lib.  Targets may link only to libraries. CMake 
is dropping the item.

and for the other binaries I get similar messages.
Using MAKE results in the follwing error:

/Users/jaschone/Downloads/gromacs-4.5.5/src/kernel/gmxdump.c:150:11: 
warning: expression result unused [-Wunused-value]

  if (state,tpx.bF) {
  ^
1 warning generated.
Undefined symbols for architecture x86_64:
  _fftwf_plan_guru_dft_r2c, referenced from:
  _fft5d_plan_3d in libmd.a(fft5d.c.o)
and then similar errors for other routines.
The complete STD.OUT and STD.ERR files for the CMAKE and the MAKE 
command were saved.

Does anyone has an idea for an solution?
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[gmx-users] g_select error


hello:

 I am going to calculate the number of water molecules within 6 A of 
residue 114 by following command:



g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 
 0.6



but it said:


WARNING: masses and atomic (Van der Waals) radii will be determined
 based on residue and atom names. These numbers can deviate
 from the correct mass and radius of the atom type.

selection parser: syntax error
selection parser: invalid selection 'resid 114 and rdist  0.6'

---
Program g_select, VERSION 4.5.5
Source code file: trajana.c, line: 1310

Input error or input inconsistency:
selection(s) could not be parsed
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

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Re: [gmx-users] Umbrella sampling - regd

2012-11-26 Thread ramesh cheerla

Dear Justin,

I am very thankful to you for your reply, you are correct, I have plotted
the histo.xvg file in wrong manner. After plotting histograms in correct
manner I have realized that my sampling is very poor as histograms and
there overlapping is restricted to some regions only, no histograms in
some areas along reaction co-ordinate.
I am not sure whether this lack of sampling is due to inappropriate
selection of pulled configurations or inappropriate pull geometry.
However I will try as per your suggestion and get back to you.

Thank you,

Regards,
Ramesh.

On Mon, Nov 26, 2012 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote:

On 11/26/12 1:03 AM, ramesh cheerla wrote:

Dear Gromacs users,

I am calculating PMF for the ion permeation through a tunnel, using
umbrella sampling. In my system I have some binding sites with ions, I
have
removed some ions from binding sites before pulling and In pulling
simulations have pullaed pulled the adjacent ions to the vacant binding
site (tunnel is aligned along Y- axis).
for this I have used the following options in .mdp file.
; Pull code
pull= umbrella
pull_geometry = distance
pull_dim= N Y N
pull_start = yes
pull_ngroups= 1
pull_group0 = REFA
pull_rate1 = 0.01
pull_k1 = 3000 ; kJ mol^-1 nm^-2

Here pull_group0 = REFA is the ion at another binding site and
pull_group1 = ATBP is the atom that I am pulling to the vacant site.
In next step I have performed umbrella sampling simulations to the
selected
configurations using the following options :
; Pull code
pull= umbrella
pull_geometry = distance ; simple distance increase
pull_dim= N Y N
pull_start = yes ; define initial COM distance 0
pull_ngroups= 1
pull_group0 = REFA
pull_group1 = ATBP
pull_init1 = 0
pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 3000 ; kJ mol^-1 nm^-2
pull_nstxout= 100
pull_nstfout= 100
After that I have constructed PMF profile using Gromacs tool g_wham,
while using g_wham I am getting the following warnings,
WARNING, no data point in bin 34 (z=0.889382) !
You may not get a reasonable profile. Check your histograms!
I have checked my histograms instead of one histogram for each
configuration with perfect overlapping, I am getting only one histogram.

You're probably just plotting the file wrong.

xmgrace -nxy histo.xvg

Here I am sending the link that containing PMF profile and histogram that
have obtained.
http://researchweb.iiit.ac.in/**~bipin.singh/pmf.jpghttp://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg
http://researchweb.iiit.ac.in/**~bipin.singh/hist.jpghttp://researchweb.iiit.ac.in/~bipin.singh/hist.jpg

The PMF suggests massive undersampling (or complete lack of sampling) in
several areas.

the weired thing that I have observed in my pulling simulations is that I
have expected motion of ion in positive Y-direction for my pull parameters
but it is moving in negative Y- direction.
Can anybody please suggest me a solution for this, Am I following
correct
protocol to get PMF of my system, is there any better method that suits
for
my system.

If you are trying to see a complete translocation of an ion through a
channel, the distance geometry is inappropriate, as it does not deal
correctly with the change of sign for the vector between the reference and
pulled group, IIRC. Try position geometry and associated settings.

-Justin

--
==**==

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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==**==
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Re: [gmx-users] Bonds - force constant for given Beads

2012-11-26 Thread André Farias de Moura

the distance distribution should be given by the Boltzmann factor of the
potential energy function between the beads, assigning V(r)=0 for the most
probable distance in your histogram. that's what you get when you take a
molecule in vacuum and for instance you compare the dihedral distribution
with the dihedral potential, the distribution is just exp[-U(theta)/RT],
except maybe for an additive constant.

you should be aware that the distribution may change appreciably depending
on the environment, so this approach may be tricky: you may include
implicit solvent effects on your bonded parameters and then you would end
up with a forcefield that counts twice the solvent effects on the internal
structure if you add explicit solvent in your model system.

I hope it helps.

Andre

On Mon, Nov 26, 2012 at 2:06 PM, Steven Neumann s.neuman...@gmail.comwrote:

 Dear Gmx Users,


 I am planning to build coarse grained model based on the all atom
 simulation. I created (using VMD) beads representing 2-4 atoms of my
 protein chain. I want to extract bonded parameters. The equilibrium
 lenght for bonds (between specified beads) would be the average over
 the equilibrium from all atom simulation using g_dist between Centre
 of Mass of group of atoms belonging to given bead.

 My question: How can I extract the force constant for the bonds from
 all atom simulation between those beads?

 Thank you,

 Steven
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_

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Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] Installation problems with MacOS 10.7.5

2012-11-26 Thread Mark Abraham

You need to name libraries with FFTW3F_LIBRARIES, not the library path.
That explains the dropped dependency and subsequent problems.

Mark

On Mon, Nov 26, 2012 at 4:19 PM, Stefan Jasconek
stjas...@students.uni-mainz.de wrote:

Dear Users,
I have problems with the installation of GROMACS 4.5.5 on MacOS 10.7.5.
GCC version 4.2.1
FFTW is: FFTW-3.3.2.
The CMAke command
cmake -DGMX_THREAD_MPI=OFF \
-DFFTW3F_INCLUDE_DIR=$FFTWDIR/**include \
-DFFTW3F_LIBRARIES=$FFTWDIR/**lib \
-DGMX_X11=OFF \
-DCMAKE_INSTALL_PREFIX=$(pwd) \
-DGMX_MPI=OFF \
-DGMX_THREADS=OFF \
-DBUILD_SHARED_LIBS=OFF \
/Users/jaschone/Downloads/**gromacs-4.5.5
Where CCDIR is the location of the GCC binary, FFTWDIR is the location of
the FFTW stuff.

I get the following error mesage:
WARNING: Target md requests linking to directory
/Users/jaschone/progs/lib. Targets may link only to libraries. CMake is
dropping the item.
and for the other binaries I get similar messages.
Using MAKE results in the follwing error:

/Users/jaschone/Downloads/**gromacs-4.5.5/src/kernel/**gmxdump.c:150:11:
warning: expression result unused [-Wunused-value]
if (state,tpx.bF) {
^
1 warning generated.
Undefined symbols for architecture x86_64:
_fftwf_plan_guru_dft_r2c, referenced from:
_fft5d_plan_3d in libmd.a(fft5d.c.o)
and then similar errors for other routines.
The complete STD.OUT and STD.ERR files for the CMAKE and the MAKE command
were saved.
Does anyone has an idea for an solution?
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[gmx-users] g_select error



hello:

 I am going to calculate the number of water molecules within 6 A of
residue 114 by following command:


g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist
 0.6


but it said:


WARNING: masses and atomic (Van der Waals) radii will be determined
 based on residue and atom names. These numbers can deviate
 from the correct mass and radius of the atom type.

selection parser: syntax error
selection parser: invalid selection 'resid 114 and rdist  0.6'

---
Program g_select, VERSION 4.5.5
Source code file: trajana.c, line: 1310

Input error or input inconsistency:
selection(s) could not be parsed
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)




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[gmx-users] Re: Bonds - force constant for given Beads

2012-11-26 Thread Thomas Schlesier


A good start might be:
Phys. Chem. Chem. Phys., 2011, 13, 10437–10448
This paper is about hybrid-models (mixing CG and AA). But they discuss 
'boltzmann inversion' and 'force matching', which are both methods to 
obtain CG-potentials.
Since they use small molecules it focusses on nonbonded interactions, 
but one can probably transfer the methods to bonded interactions.

Greetings
Thomas



Am 26.11.2012 18:45, schrieb gmx-users-requ...@gromacs.org:

the distance distribution should be given by the Boltzmann factor of the
potential energy function between the beads, assigning V(r)=0 for the most
probable distance in your histogram. that's what you get when you take a
molecule in vacuum and for instance you compare the dihedral distribution
with the dihedral potential, the distribution is just exp[-U(theta)/RT],
except maybe for an additive constant.

you should be aware that the distribution may change appreciably depending
on the environment, so this approach may be tricky: you may include
implicit solvent effects on your bonded parameters and then you would end
up with a forcefield that counts twice the solvent effects on the internal
structure if you add explicit solvent in your model system.

I hope it helps.

Andre

On Mon, Nov 26, 2012 at 2:06 PM, Steven Neumanns.neuman...@gmail.comwrote:


Dear Gmx Users,


I am planning to build coarse grained model based on the all atom
simulation. I created (using VMD) beads representing 2-4 atoms of my
protein chain. I want to extract bonded parameters. The equilibrium
lenght for bonds (between specified beads) would be the average over
the equilibrium from all atom simulation using g_dist between Centre
of Mass of group of atoms belonging to given bead.

My question: How can I extract the force constant for the bonds from
all atom simulation between those beads?

Thank you,

Steven


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Re: [gmx-users] How to avoid adding ions close to ligand

2012-11-26 Thread David van der Spoel


On 2012-11-26 21:28, Yun Shi wrote:

Hi everyone,

I am doing conventional MD of a protein-ligand system with a mobile
loop as part of the binding site.

Presumably, the positive Arg side chain on the mobile loop will
eventually move towards the negative carboxylic group on my ligand.
But I found the addition of NaCl (0.15 M conc.) had some effect on
this movement, since the random addition could put Na+ or Cl- ions
between the mobile loop and my ligand.

I tried generating a index containing only SOL far not close to my
ligand, but apparently genion requires a continuous solvent group. So
is there any other way to achieve this? Trying different numbers for
-seed option seems inefficient and is dependent on luck.

Thanks,
Yun


Maybe your assumption is wrong?

Run a long MD simulation and you will find out.

--
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Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] g_select error