date:20121004


On 4/10/2012 5:10 PM, Albert wrote:

hello:

  I found that the .trr from mdrun output is really much huger than 
the .xtc file. However, most people would like to generate the .trr 
file and then convert it into .xtc file.


See 
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume


Mark
I am just wondering can we generate the .xtc file directly from mdrun 
command like:


mdrun -s md.tpr -o md.xtc


I also found that the CHARMM36 FF (charmm36.ff_4.5.4_ref.tgz 
http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz) 
in gromac website seems to be update, I am wondering is it the latest 
CHARMM37 FF?


THX
Albert


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[gmx-users] Segmentation fault, mdrun_mpi

2012-10-04 Thread Ladasky

So I have spent the past few weeks debugging my equilibration protocols,
which were an odd hybrid of examples ranging from GROMACS 3.3 up to GROMACS
4.5.  I have cleaned out old code.  I added an in vacuo energy minimization
step for the protein without solvent, and a missing NVT step after solvent
is defined.  I have dimly grasped that, as long as you don't require
compatibility with an older simulation, the V-rescale thermostat is the
current recommended choice, and that switching thermostats (unlike
barostats) can cause instabilities.  I now know how to examine and graph
macroscopic system parameters to assess stability.  I think that everything
should be looking good right now -- except that it isn't, not quite.

When I finally start the production MD runs, I have received two
segmentation faults on two different test structures.  They take a LONG time
to appear -- over 1,070,000 iterations on one run, and over 2,360,000
iterations on another.  On top of that, I'm not getting my usual error
messages -- PME errors, or SETTLE errors.  I'm not getting a dump of the
last frame of my simulation.

I had enough trouble accepting that my simulation parameters were set up
incorrectly when I had failures 100,000 steps after starting the production
MD run.  Am I really supposed to believe that I still have instability
problems?

Here is the terminal output from one run (executing mdrun_mpi):

Reading file test-prep.tpr, VERSION 4.5.4 (single precision)
Making 1D domain decomposition 5 x 1 x 1
starting mdrun 'Protein t=   0.0 in water'
250 steps,   5000.0 ps.
[john-linux:09596] *** Process received signal ***
[john-linux:09596] Signal: Segmentation fault (11)
[john-linux:09596] Signal code: Address not mapped (1)
[john-linux:09596] Failing at address: 0x3e950840
[john-linux:09596] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10060)
[0x7f8a8ad5c060]
[john-linux:09596] [ 1] /usr/lib/libgmx_mpi.openmpi.so.6(+0x1f9670)
[0x7f8a8b413670]
[john-linux:09596] *** End of error message ***
--
mpirun noticed that process rank 2 with PID 9596 on node john-linux exited
on signal 11 (Segmentation fault).
--


The .log file does NOT contain any error messages, indicating any
instability.  The last entry in the log file is a long chain of energy
status report blocks.  Here's the last one:

DD  step 1078799 load imb.: force  1.8%

   Step   Time Lambda
1078800 2157.60.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
2.07623e+038.42439e+026.03967e+02   -2.12322e+021.95589e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
8.12766e+04   -9.12661e+02   -5.96406e+05   -4.40546e+04   -5.37227e+05
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
9.76293e+04   -4.39598e+053.10969e+02   -7.72781e+013.95185e+01
   Constr. rmsd
1.90839e-05


I'm not a low-level programmer, and so I don't have to deal with this much,
but... a segmentation fault generally indicates that a program is trying to
write outside of its allocated memory block.  The third line of the error
message sent to the shell would seem to indicate exactly that.  That doesn't
actually sound like it has anything to do with my simulation being unstable. 
(However, with applications written in C, I'm willing to believe anything.) 
I did check on my memory usage.  I have 8 GB of RAM on my system, running
Ubuntu Linux 11.10, AMD 64-bit.  At most, I'm using a bit more than half of
my RAM (I have other, undemanding applications open besides my GROMACS
terminal windows, and I also reserved one CPU core to run those apps).  I
think that I should be fine.

If they would help, I can repost my cleaned-up MDP files. I can post graphs
of potential, pressure, temperature, density, etc., from any phase in my
protocol.   Or you could just take my word for it that all of these
parameters converge nicely during my equilibration procedure, and then
remain stable throughout the production MD run.  My target temperature is
310 K (37 C), and I get very close to that value on average.  My average
pressure and density readings are both a bit lower than my targets (0.80 bar
and 988 kg/m^3, respectively), but they are consistent.  I have examined a
series of snapshots of my protein.  It isn't undergoing any radical
movements.

My systems are on the small side, under 50,000 atoms.  It's all amino acids
and water molecules.

Puzzled once again.  Thanks for your advice!



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Re: [gmx-users] Dssp core dumped

2012-10-04 Thread Tsjerk Wassenaar

Hi Rama,

I bet that wasn't the only output you got. Two things can usually
happen with do_dssp. Either you chose the wrong group for analysis, or
there is a problem with the version of DSSP. Probably the latter: DSSP
syntax changed recently, and I think that GMX 4.5.5 can't deal with
that. There should be capital punishment on syntax changes on such
programs... Try digging up an older version of DSSP.

Cheers,

Tsjerk

On Thu, Oct 4, 2012 at 11:18 AM, rama david ramadavidgr...@gmail.com wrote:
 hi Gromacs Friend i Install dssp 2.0.4 .
 I am using gromacs 4.5.5
 I put dssp in /usr/local/bin

   I  try with export DSSP=/usr/local/bin/dssp

 When Run dssp with simple pdb file it run
 but when I run do_dssp command i got following output..


 Segmentation fault (core dumped)

 (dssp -h
 DSSP 2.0.4 options:
   -h [ --help ] Display help message )


 I also goes through archive but not find out the answer.


 Please tel me how to figure out these problem


 With best wishes and regards..
 rama david
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post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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[gmx-users] Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

2012-10-04 Thread Emma Eriksson

Dear all,

I am using the pull code in Gromacs 4.5.5 to constrain the distance in one 
direction (z) between a small molecule and a lipid bilayer. I run separate 
simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. 
The pull parameters are the following: 

pull   = constraint
pull_geometry   = cylinder
pull_r1  = 1.0
pull_r0  = 1.5
pull_group0   = DMPC
pull_group1   = 2
pull_vec1  = 0 0 1
pull_init1   = x

I have previously been using the same methodology in 4.0.5 without problems. 
When i run grompp in 4.5.5 I get the following error:

Fatal error:
Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size 
(3.012310)

The source of the first value, which should be the distance of pull group 1 is 
for me unknown. A value of ~4 is generated for all systems no matter what z 
distance is actually betwen the two groups (0-4 nm), so the value has no 
connection to the z distance between the groups. The second value is 0.5 times 
the x box length. I have read through pull.c, but I cannot find an explanation 
to why the x direction seems to be considered and not the z direction. When I 
run grompp with pull_geometry = distance or direction together with pull_dim = 
N N Y there is no problem.  

As I am not sure of the source of this error when running with cylinder I do 
not know if it is only related to the check or if the following simulation 
would be affected if I uncomment the check. 

Any suggestions to why this is happening and what I can do about it?
Thanks!

Best regards,
Emma --
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Re: [gmx-users] Interaction study for peptide-receptor..




On 10/4/12 2:01 AM, rama david wrote:

Hi gromacs Friends,
 I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up  of  4 amino acids. I know the interaction pattern of
peptide and receptor.
I plan to mutate single residue each at a time and  run 4 simulation .
So I will have the 4 different simulation that contain the mutated residues
and the wild one.


Then afterward from the interaction energy I want to select the peptide
which is showing
stronger interaction than others.

As  mention I know the binding site, If I freeze the remaining portion in
receptor
that not involved in binding , Is it going to affect my screening process
???



Potentially.  Do you know that the binding interactions and the mutations will 
only perturb local residues?  Do you know that there are no long-range motions 
to be considered?


I think you gain very little by freezing portions of the system, and risk more 
than you gain.


-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] Interaction study for peptide-receptor..

thank you Justin for reply.

I dont know about long range interactions.
But as I freeze the group I think it will improve my computational speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??

Should I do Essential Dynamics ??? or Principle component analysis ???

Would you suggest me any general protocol for such work??

Thank you in Advance

With Best Wishes and regards.
Rama David

On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:

On 10/4/12 2:01 AM, rama david wrote:

Hi gromacs Friends,
I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up of 4 amino acids. I know the interaction pattern of
peptide and receptor.
I plan to mutate single residue each at a time and run 4 simulation .
So I will have the 4 different simulation that contain the mutated
residues
and the wild one.

Then afterward from the interaction energy I want to select the peptide
which is showing
stronger interaction than others.

As mention I know the binding site, If I freeze the remaining portion in
receptor
that not involved in binding , Is it going to affect my screening process
???

Potentially. Do you know that the binding interactions and the mutations
will only perturb local residues? Do you know that there are no long-range
motions to be considered?

I think you gain very little by freezing portions of the system, and risk
more than you gain.

-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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Re: [gmx-users] Interaction study for peptide-receptor..

2012-10-04 Thread francesco oteri

Hi,
as far as I know, freezing just set velocities to 0 so you gain nothing
freezing atoms.

By the way, have you tried docking? It takes into account multiple
conformation and
orientation of the peptide and, depending upon the implemented algorithm,
also
protein sidechain orientation.

Francesco


2012/10/4 rama david ramadavidgr...@gmail.com

 thank you Justin for reply.

 I dont know about long range interactions.
 But as I freeze the group I think it will improve my computational speed.
 So is there any way to find out or decide which group should be
 freeze, and which group should affect my interaction most probably??

 Should I do Essential Dynamics ??? or Principle component analysis ???

 Would you suggest me any general protocol for such work??

 Thank you in Advance


 With Best Wishes and regards.
 Rama David

 On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:

 
 
  On 10/4/12 2:01 AM, rama david wrote:
 
  Hi gromacs Friends,
   I want to do peptide-receptor ( Protein) interaction
  study.Receptor consist a single chain.
  Peptide is made up  of  4 amino acids. I know the interaction pattern of
  peptide and receptor.
  I plan to mutate single residue each at a time and  run 4 simulation .
  So I will have the 4 different simulation that contain the mutated
  residues
  and the wild one.
 
 
  Then afterward from the interaction energy I want to select the peptide
  which is showing
  stronger interaction than others.
 
  As  mention I know the binding site, If I freeze the remaining portion
 in
  receptor
  that not involved in binding , Is it going to affect my screening
 process
  ???
 
 
  Potentially.  Do you know that the binding interactions and the mutations
  will only perturb local residues?  Do you know that there are no
 long-range
  motions to be considered?
 
  I think you gain very little by freezing portions of the system, and risk
  more than you gain.
 
  -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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
  ==**==
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] Interaction study for peptide-receptor..

Hi francesco,

Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto the
mark.

Is the freezing of group can affect my system?? How much efficiency I get
by these work??
As these group are going to freeze in four simulation so if it affect one
ligand it  affect other
ligand also.

I read article that did the work like me ,
they sliced the binding residues and  used the inert solid sphere to
support binding residues
instead of the freezing group other group.

I think both way should have same effect..Am I right or wrong??

If you have any other way please suggest it..

With best wishes and regards
Rama david


On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
francesco.ot...@gmail.comwrote:

 Hi,
 as far as I know, freezing just set velocities to 0 so you gain nothing
 freezing atoms.

 By the way, have you tried docking? It takes into account multiple
 conformation and
 orientation of the peptide and, depending upon the implemented algorithm,
 also
 protein sidechain orientation.

 Francesco


 2012/10/4 rama david ramadavidgr...@gmail.com

  thank you Justin for reply.
 
  I dont know about long range interactions.
  But as I freeze the group I think it will improve my computational speed.
  So is there any way to find out or decide which group should be
  freeze, and which group should affect my interaction most probably??
 
  Should I do Essential Dynamics ??? or Principle component analysis ???
 
  Would you suggest me any general protocol for such work??
 
  Thank you in Advance
 
 
  With Best Wishes and regards.
  Rama David
 
  On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:
 
  
  
   On 10/4/12 2:01 AM, rama david wrote:
  
   Hi gromacs Friends,
I want to do peptide-receptor ( Protein) interaction
   study.Receptor consist a single chain.
   Peptide is made up  of  4 amino acids. I know the interaction pattern
 of
   peptide and receptor.
   I plan to mutate single residue each at a time and  run 4 simulation .
   So I will have the 4 different simulation that contain the mutated
   residues
   and the wild one.
  
  
   Then afterward from the interaction energy I want to select the
 peptide
   which is showing
   stronger interaction than others.
  
   As  mention I know the binding site, If I freeze the remaining portion
  in
   receptor
   that not involved in binding , Is it going to affect my screening
  process
   ???
  
  
   Potentially.  Do you know that the binding interactions and the
 mutations
   will only perturb local residues?  Do you know that there are no
  long-range
   motions to be considered?
  
   I think you gain very little by freezing portions of the system, and
 risk
   more than you gain.
  
   -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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  
   ==**==
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 --
 Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] Interaction study for peptide-receptor..




On 10/4/12 8:08 AM, rama david wrote:

Hi francesco,

Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto the
mark.

Is the freezing of group can affect my system?? How much efficiency I get
by these work??


You will not get any improvement in computational efficiency, and if you use 
NPT, you will get artifacts.  One can potentially speed up a calculation using 
energygrp_excl, but that's layering assumptions upon assumptions, which I think 
is bad news.  You've said you don't know if long-range interactions play a role. 
 That, to me, means you absolutely cannot justify any sort of freezing.


The fact that docking did not produce very good results is unsurprising.  The 
largely rigid treatment of proteins in docking leaves much to be desired.  This 
is yet another argument against freezing parts of your protein - if docking did 
not produce good results, why would you expect a mostly frozen MD system to 
perform much better?



As these group are going to freeze in four simulation so if it affect one
ligand it  affect other
ligand also.

I read article that did the work like me ,
they sliced the binding residues and  used the inert solid sphere to
support binding residues
instead of the freezing group other group.

I think both way should have same effect..Am I right or wrong??



I don't really understand what it is the other group did, aside from perhaps 
modeling a subsystem.  Still, I don't think such lengths are necessary or 
inherently beneficial.



If you have any other way please suggest it..



I see no reason not to treat this system with normal MD protocols.


-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] Interaction study for peptide-receptor..

2012-10-04 Thread francesco oteri

2012/10/4 rama david ramadavidgr...@gmail.com

 Hi francesco,

 Thank you For reply.
 I did docking but the result are not so impressive.


What does it mean not so impressive? I mean, do you have experimental
data
and the comparison with docking doesn't agree with experiments? Have you
generated
a sufficient number of complexes (say 100 or more)?

I used vina and autodock.
 I also did virtual screening in autodock but the result are not upto the
 mark.

 Is the freezing of group can affect my system?? How much efficiency I get
 by these work??


It will change a lot the dynamics of your system and I don't think
calculations
will be more efficient!


 As these group are going to freeze in four simulation so if it affect one
 ligand it  affect other
 ligand also.

 I read article that did the work like me ,
 they sliced the binding residues and  used the inert solid sphere to
 support binding residues
 instead of the freezing group other group.

 I think both way should have same effect..Am I right or wrong??

 If you have any other way please suggest it..


If you already have docking complexes, you can pick up one complex for each
peptide, to run an MD, or Free Energy  calculations.
It strongly depends by the experimentale data you have and what is the
target
of your work.



 With best wishes and regards
 Rama david


 On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
 francesco.ot...@gmail.comwrote:

  Hi,
  as far as I know, freezing just set velocities to 0 so you gain nothing
  freezing atoms.
 
  By the way, have you tried docking? It takes into account multiple
  conformation and
  orientation of the peptide and, depending upon the implemented algorithm,
  also
  protein sidechain orientation.
 
  Francesco
 
 
  2012/10/4 rama david ramadavidgr...@gmail.com
 
   thank you Justin for reply.
  
   I dont know about long range interactions.
   But as I freeze the group I think it will improve my computational
 speed.
   So is there any way to find out or decide which group should be
   freeze, and which group should affect my interaction most probably??
  
   Should I do Essential Dynamics ??? or Principle component analysis ???
  
   Would you suggest me any general protocol for such work??
  
   Thank you in Advance
  
  
   With Best Wishes and regards.
   Rama David
  
   On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:
  
   
   
On 10/4/12 2:01 AM, rama david wrote:
   
Hi gromacs Friends,
 I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up  of  4 amino acids. I know the interaction
 pattern
  of
peptide and receptor.
I plan to mutate single residue each at a time and  run 4
 simulation .
So I will have the 4 different simulation that contain the mutated
residues
and the wild one.
   
   
Then afterward from the interaction energy I want to select the
  peptide
which is showing
stronger interaction than others.
   
As  mention I know the binding site, If I freeze the remaining
 portion
   in
receptor
that not involved in binding , Is it going to affect my screening
   process
???
   
   
Potentially.  Do you know that the binding interactions and the
  mutations
will only perturb local residues?  Do you know that there are no
   long-range
motions to be considered?
   
I think you gain very little by freezing portions of the system, and
  risk
more than you gain.
   
-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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
   
==**==
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  Cordiali saluti, Dr.Oteri Francesco
  --
  gmx-users

Re: [gmx-users] Re: Fatal error: Atomtype F not found




On 10/3/12 11:41 PM, shika wrote:

Thanks for fast reply.I am very new to this and yes I am confused

my itp file is :

; solvent_HFI.gro.top created by rdparm2gmx.pl Sat May 28 10:25:18 MYT 2005
;
;
[ moleculetype ]
; Namenrexcl
solute 3

[ atoms ]
;   nr   type  resnr   residue   atomcgnr  charge
mass typeBchargeB
  1 opls_164  1   HFI  F   1  -0.234745 
19.00
  2 opls_161  1   HFI  C   2   0.705532 
12.00
  3 opls_164  1   HFI F1   3  -0.205102 
19.00
  4 opls_164  1   HFI F2   4  -0.237125 
19.00
  5 opls_158  1   HFI C1   5  -0.119035 
12.00
  6 opls_078  1   HFI  O   6  -0.600958 
16.00
  7 opls_079  1   HFI H1   7   0.468121  
1.00
  8 opls_140  1   HFI  H   8   0.141115  
1.00
  9 opls_161  1   HFI C2   9   0.786317 
12.00
 10 opls_164  1   HFI F4  10  -0.230854 
19.00
 11 opls_164  1   HFI F5  11  -0.266972 
19.00
 12 opls_164  1   HFI F3  12  -0.206295 
19.00

[ bonds ]
;  aiaj funct
 5 8 1
 6 7 1
 1 2 1
 2 3 1
 2 4 1
 2 5 1
 5 6 1
 5 9 1
 910 1
 911 1
 912 1

[ pairs ]
;  aiaj funct
  1  8  1
  2  7  1
  3  8  1
  4  8  1
  7  8  1
  7  9  1
  8 10  1
  8 11  1
  8 12  1
  1  6  1
  1  9  1
  2 10  1
  2 11  1
  2 12  1
  3  6  1
  3  9  1
  4  6  1
  4  9  1
  6 10  1
  6 11  1
  6 12  1

[ angles ]
;  aiajak funct
 2 5 8 1
 5 6 7 1
 6 5 8 1
 8 5 9 1
 1 2 3 1
 1 2 4 1
 1 2 5 1
 2 5 6 1
 2 5 9 1
 3 2 4 1
 3 2 5 1
 4 2 5 1
 5 910 1
 5 911 1
 5 912 1
 6 5 9 1
10 911 1
10 912 1
11 912 1

[ dihedrals ]
;i  j   k  l func   
 1258  3
 2567  3
 3258  3
 4258  3
 7658  3
 7659  3
 85910 3
 85911 3
 85912 3
 1256  3
 1259  3
 25910 3
 25911 3
 25912 3
 3256  3
 3259  3
 4256  3
 4259  3
 65910 3
 65911 3
 65912 3

I would be grateful if you could highlight things that need to be edited.


There is no atomtype F referenced in this topology, so the source of the error 
is still unclear.



One more thing,is OPLSAA forcefield suitable for my non standard molecule?



Any force field can be used for any molecule, provided the parameterization was 
done thoroughly and evaluated properly.  The header of your topology suggests 
you used an AMBER conversion script, so you may be mixing and matching 
parameters here, which is a bad idea.


-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] hexafluoroisopropanol




On 10/4/12 1:34 AM, Nur Syafiqah Abdul Ghani wrote:

Hi Guys,

Need your help urgently.
I already read a lot of paper about molecular dynamics simulation
which relate work as mine.The main point is to create the mix solvent.
The co-solvent is hexafluoroisopropanol and a lot of researcher cited
the journal name 1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular
dynamics simulations by Fioroni.

So my question,is the molecule already have a pdb structure?Have
anyone dealing with this compound?


Constructing a coordinate file for a small organic molecule is rather simple 
with any number of tools.


http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources


Because im currently lost due to my HFIP pdb is wrong and the atom
type of F is not recognized and the force field i used is OPLSAA but
right now i think i need to change it to the
GROMOS96..Your advise are highly appreciate..



You should not presume that one force field is inherently better than another 
for an arbitrary molecule that is not already parameterized.  One could produce 
reliable parameters for any force field, provided care is taken to derive and 
evaluate them properly.


There seem to be two threads with nearly identical problems.  Perhaps you can 
cross-reference some information with the other active thread.


-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] Interaction study for peptide-receptor..

Thank you justin and franscisco,
I have practical data that claim that only a particular residue that is c
terminal residue  is
involve in binding.
  but when I generate the docking data other residues most of the time
comes to play.
I know the binding of natural ligand ( peptide ) and the position.
so I think if I mutate only these residue and simulate the system I will
get the
structure that is more active. In natural ligand the C terminal is playing
important role.


With simulation i will find interaction energy.
  That will tell me about binding affinity  ( Hope so )
These is my basic idea.

Is any other way to do the same thing..

With best wishes and regards
Rama David


On Thu, Oct 4, 2012 at 5:47 PM, francesco oteri
francesco.ot...@gmail.comwrote:

 2012/10/4 rama david ramadavidgr...@gmail.com

  Hi francesco,
 
  Thank you For reply.
  I did docking but the result are not so impressive.
 

 What does it mean not so impressive? I mean, do you have experimental
 data
 and the comparison with docking doesn't agree with experiments? Have you
 generated
 a sufficient number of complexes (say 100 or more)?

 I used vina and autodock.
  I also did virtual screening in autodock but the result are not upto the
  mark.
 
  Is the freezing of group can affect my system?? How much efficiency I get
  by these work??
 

 It will change a lot the dynamics of your system and I don't think
 calculations
 will be more efficient!


  As these group are going to freeze in four simulation so if it affect one
  ligand it  affect other
  ligand also.
 
  I read article that did the work like me ,
  they sliced the binding residues and  used the inert solid sphere to
  support binding residues
  instead of the freezing group other group.
 
  I think both way should have same effect..Am I right or wrong??
 
  If you have any other way please suggest it..
 

 If you already have docking complexes, you can pick up one complex for each
 peptide, to run an MD, or Free Energy  calculations.
 It strongly depends by the experimentale data you have and what is the
 target
 of your work.


 
  With best wishes and regards
  Rama david
 
 
  On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
  francesco.ot...@gmail.comwrote:
 
   Hi,
   as far as I know, freezing just set velocities to 0 so you gain nothing
   freezing atoms.
  
   By the way, have you tried docking? It takes into account multiple
   conformation and
   orientation of the peptide and, depending upon the implemented
 algorithm,
   also
   protein sidechain orientation.
  
   Francesco
  
  
   2012/10/4 rama david ramadavidgr...@gmail.com
  
thank you Justin for reply.
   
I dont know about long range interactions.
But as I freeze the group I think it will improve my computational
  speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??
   
Should I do Essential Dynamics ??? or Principle component analysis
 ???
   
Would you suggest me any general protocol for such work??
   
Thank you in Advance
   
   
With Best Wishes and regards.
Rama David
   
On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu
 wrote:
   


 On 10/4/12 2:01 AM, rama david wrote:

 Hi gromacs Friends,
  I want to do peptide-receptor ( Protein) interaction
 study.Receptor consist a single chain.
 Peptide is made up  of  4 amino acids. I know the interaction
  pattern
   of
 peptide and receptor.
 I plan to mutate single residue each at a time and  run 4
  simulation .
 So I will have the 4 different simulation that contain the mutated
 residues
 and the wild one.


 Then afterward from the interaction energy I want to select the
   peptide
 which is showing
 stronger interaction than others.

 As  mention I know the binding site, If I freeze the remaining
  portion
in
 receptor
 that not involved in binding , Is it going to affect my screening
process
 ???


 Potentially.  Do you know that the binding interactions and the
   mutations
 will only perturb local residues?  Do you know that there are no
long-range
 motions to be considered?

 I think you gain very little by freezing portions of the system,
 and
   risk
 more than you gain.

 -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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-users

Re: [gmx-users] Interaction study for peptide-receptor..




On 10/4/12 8:40 AM, rama david wrote:

Thank you justin and franscisco,
I have practical data that claim that only a particular residue that is c
terminal residue  is
involve in binding.
   but when I generate the docking data other residues most of the time
comes to play.
I know the binding of natural ligand ( peptide ) and the position.
so I think if I mutate only these residue and simulate the system I will
get the
structure that is more active. In natural ligand the C terminal is playing
important role.


With simulation i will find interaction energy.


Interaction energy is a very vague term that people often use fairly 
erroneously to justify their findings.  Force fields are not necessarily 
guaranteed to produce anything meaningful from the sum of nonbonded terms.



   That will tell me about binding affinity  ( Hope so )


More sophisticated free energy calculations would be necessary to determine 
binding affinity or free energy of binding.


-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] Interaction study for peptide-receptor..

2012-10-04 Thread Thomas Evangelidis

I don't think AutoDock and Vina are suitable for peptide docking. I would
first try the FlexPepDocking module of Rosetta which does ab initio folding
of the peptide on the receptor, while moving the side-chains of the protein
but leaves its backbone intact. Rosetta implements a knowledge-based
scoring, which has been specifically designed for this task and is as fast
as Vina or AutoDock.

I would first do that and if I wouldn't get any reasonable results then I
would move to MD starting from the top scored protein-peptide complexes
created by Rosetta.

Thomas


On 4 October 2012 15:08, rama david ramadavidgr...@gmail.com wrote:

 Hi francesco,

 Thank you For reply.
 I did docking but the result are not so impressive.
 I used vina and autodock.
 I also did virtual screening in autodock but the result are not upto the
 mark.

 Is the freezing of group can affect my system?? How much efficiency I get
 by these work??
 As these group are going to freeze in four simulation so if it affect one
 ligand it  affect other
 ligand also.

 I read article that did the work like me ,
 they sliced the binding residues and  used the inert solid sphere to
 support binding residues
 instead of the freezing group other group.

 I think both way should have same effect..Am I right or wrong??

 If you have any other way please suggest it..

 With best wishes and regards
 Rama david


 On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
 francesco.ot...@gmail.comwrote:

  Hi,
  as far as I know, freezing just set velocities to 0 so you gain nothing
  freezing atoms.
 
  By the way, have you tried docking? It takes into account multiple
  conformation and
  orientation of the peptide and, depending upon the implemented algorithm,
  also
  protein sidechain orientation.
 
  Francesco
 
 
  2012/10/4 rama david ramadavidgr...@gmail.com
 
   thank you Justin for reply.
  
   I dont know about long range interactions.
   But as I freeze the group I think it will improve my computational
 speed.
   So is there any way to find out or decide which group should be
   freeze, and which group should affect my interaction most probably??
  
   Should I do Essential Dynamics ??? or Principle component analysis ???
  
   Would you suggest me any general protocol for such work??
  
   Thank you in Advance
  
  
   With Best Wishes and regards.
   Rama David
  
   On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote:
  
   
   
On 10/4/12 2:01 AM, rama david wrote:
   
Hi gromacs Friends,
 I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up  of  4 amino acids. I know the interaction
 pattern
  of
peptide and receptor.
I plan to mutate single residue each at a time and  run 4
 simulation .
So I will have the 4 different simulation that contain the mutated
residues
and the wild one.
   
   
Then afterward from the interaction energy I want to select the
  peptide
which is showing
stronger interaction than others.
   
As  mention I know the binding site, If I freeze the remaining
 portion
   in
receptor
that not involved in binding , Is it going to affect my screening
   process
???
   
   
Potentially.  Do you know that the binding interactions and the
  mutations
will only perturb local residues?  Do you know that there are no
   long-range
motions to be considered?
   
I think you gain very little by freezing portions of the system, and
  risk
more than you gain.
   
-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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
   
==**==
--
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  --
  Cordiali

Re: [gmx-users] Coordinate file for lipid bilayer

2012-10-04 Thread James Starlight

Dear Felipe,

thanks for advise. Does the Packmol software suitable for generation
coordinates of the bergers ( for gromos 56 ff) lipids ? As I know
CHARMM-GUI membrane builder is suitable for only CHARMM force field
lipids.

James

2012/10/4 Felipe Pineda, PhD luis.pinedadecas...@lnu.se:
 To generate starting (non-equilibrated) bilayer structures for use in MD
 simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/.
 Otherwise, for conventional lipids CHARMM-GUI membrane builder
 (http://www.charmm-gui.org/?doc=input/membrane).

 Hope it helps!

 Felipe


 On 10/04/2012 07:46 AM, James Starlight wrote:

 Justin,


 lastly, is there any other ways to obtain bilayers of desired
 dimensions started from just one lipid oriented in desired way for
 instance?


 James

 2012/10/3, Justin Lemkul jalem...@vt.edu:


 On 10/3/12 12:38 PM, James Starlight wrote:

 Justin,

 thanks for advises.

 Finally how I could effectively reduce size of my system (in x and y )
 to the defined pbc box size ( see picture to the previous comment) ?

 I've noticed that increasing of x and y to the 12 nm I obtain ideal
 shape of the bilayer without miss-matches of the left and right sizes.
 But when I try to decrease dimensions of that system from 12 to 8 nm

 genbox -cs xz.gro -box 8.04542 8.04542 10.19156

 I've obtained the system with the broadered water layers again ( as in
 the picture which I've shown).

 My advice is still the same - you need box vectors that are compatible
 with
 both
 a sensible water layer and membrane leaflets.

 -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] Coordinate file for lipid bilayer

2012-10-04 Thread Felipe Pineda, PhD


Hi,

packmol generates just coordinates (pdb format) for optimized packing 
arrangements of whatever molecule you provide as input. It's up to you 
to parameterize the resulting model. CHARMM-GUI has a library of 
conventional (phospho)lipids and generates the input for CHARMM 
equilibration of the bilayer model built with those lipids. But, you 
should inspect by yourself the corresponding sites.


Felipe

On 10/04/2012 03:11 PM, James Starlight wrote:

Dear Felipe,

thanks for advise. Does the Packmol software suitable for generation
coordinates of the bergers ( for gromos 56 ff) lipids ? As I know
CHARMM-GUI membrane builder is suitable for only CHARMM force field
lipids.

James



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Re: [gmx-users] Interaction study for peptide-receptor..

Thank you  for reply,
 I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the  receptor binding site and used the the solid support
to the binding site and did simulation.
   So if I freeze  the group is it will ok ??
Is it possible in gromacs to fix the residue on solid immobilized surface.
If it is how to do it??

my question is How to decide which group are remove and which group should
keep in simulation.

thank you in advance
Thank you for giving your valuable time and advice to me.

With best wishes and regards,
Rama david






On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis teva...@gmail.comwrote:

 I don't think AutoDock and Vina are suitable for peptide docking. I would
 first try the FlexPepDocking module of Rosetta which does ab initio folding
 of the peptide on the receptor, while moving the side-chains of the protein
 but leaves its backbone intact. Rosetta implements a knowledge-based
 scoring, which has been specifically designed for this task and is as fast
 as Vina or AutoDock.

 I would first do that and if I wouldn't get any reasonable results then I
 would move to MD starting from the top scored protein-peptide complexes
 created by Rosetta.

 Thomas


 On 4 October 2012 15:08, rama david ramadavidgr...@gmail.com wrote:

  Hi francesco,
 
  Thank you For reply.
  I did docking but the result are not so impressive.
  I used vina and autodock.
  I also did virtual screening in autodock but the result are not upto the
  mark.
 
  Is the freezing of group can affect my system?? How much efficiency I get
  by these work??
  As these group are going to freeze in four simulation so if it affect one
  ligand it  affect other
  ligand also.
 
  I read article that did the work like me ,
  they sliced the binding residues and  used the inert solid sphere to
  support binding residues
  instead of the freezing group other group.
 
  I think both way should have same effect..Am I right or wrong??
 
  If you have any other way please suggest it..
 
  With best wishes and regards
  Rama david
 
 
  On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri
  francesco.ot...@gmail.comwrote:
 
   Hi,
   as far as I know, freezing just set velocities to 0 so you gain nothing
   freezing atoms.
  
   By the way, have you tried docking? It takes into account multiple
   conformation and
   orientation of the peptide and, depending upon the implemented
 algorithm,
   also
   protein sidechain orientation.
  
   Francesco
  
  
   2012/10/4 rama david ramadavidgr...@gmail.com
  
thank you Justin for reply.
   
I dont know about long range interactions.
But as I freeze the group I think it will improve my computational
  speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??
   
Should I do Essential Dynamics ??? or Principle component analysis
 ???
   
Would you suggest me any general protocol for such work??
   
Thank you in Advance
   
   
With Best Wishes and regards.
Rama David
   
On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu
 wrote:
   


 On 10/4/12 2:01 AM, rama david wrote:

 Hi gromacs Friends,
  I want to do peptide-receptor ( Protein) interaction
 study.Receptor consist a single chain.
 Peptide is made up  of  4 amino acids. I know the interaction
  pattern
   of
 peptide and receptor.
 I plan to mutate single residue each at a time and  run 4
  simulation .
 So I will have the 4 different simulation that contain the mutated
 residues
 and the wild one.


 Then afterward from the interaction energy I want to select the
   peptide
 which is showing
 stronger interaction than others.

 As  mention I know the binding site, If I freeze the remaining
  portion
in
 receptor
 that not involved in binding , Is it going to affect my screening
process
 ???


 Potentially.  Do you know that the binding interactions and the
   mutations
 will only perturb local residues?  Do you know that there are no
long-range
 motions to be considered?

 I think you gain very little by freezing portions of the system,
 and
   risk
 more than you gain.

 -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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] Coordinate file for lipid bilayer

2012-10-04 Thread Thomas Piggot


Hi James,

The bilayers from the CHARMM-GUI can be converted into any force field 
using a simple script. For a united-atom force field you will need to 
remove the non-polar hydrogens, rename the atoms and possibly reorder 
some of the atoms in the lipids.


As for other methods to build membranes, there are numerous different 
methods available. One of the simplest approaches is to use genconf to 
replicate a single lipid up to the desired size of membrane and perform 
and simulation to equilibrate the properties of your membrane (although 
depending upon the lipid and force field this may require simulations in 
the order of several hundreds of ns though). Another fairly simple 
method (which can also be easily used to make hexagonal membranes) is to 
self-assemble a coarse-grained membrane, map that back to an atomistic 
representation (using one of a number of available tools) and 
equilibrate. One issue using this method is that the self-assembly often 
results in uneven numbers of lipids per membrane leaflet. This, however, 
is easy to correct after the self-assembly.


Cheers

Tom

James Starlight wrote:

Dear Felipe,

thanks for advise. Does the Packmol software suitable for generation
coordinates of the bergers ( for gromos 56 ff) lipids ? As I know
CHARMM-GUI membrane builder is suitable for only CHARMM force field
lipids.

James

2012/10/4 Felipe Pineda, PhD luis.pinedadecas...@lnu.se:

To generate starting (non-equilibrated) bilayer structures for use in MD
simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/.
Otherwise, for conventional lipids CHARMM-GUI membrane builder
(http://www.charmm-gui.org/?doc=input/membrane).

Hope it helps!

Felipe


On 10/04/2012 07:46 AM, James Starlight wrote:

Justin,


lastly, is there any other ways to obtain bilayers of desired
dimensions started from just one lipid oriented in desired way for
instance?


James

2012/10/3, Justin Lemkul jalem...@vt.edu:


On 10/3/12 12:38 PM, James Starlight wrote:

Justin,

thanks for advises.

Finally how I could effectively reduce size of my system (in x and y )
to the defined pbc box size ( see picture to the previous comment) ?

I've noticed that increasing of x and y to the 12 nm I obtain ideal
shape of the bilayer without miss-matches of the left and right sizes.
But when I try to decrease dimensions of that system from 12 to 8 nm

genbox -cs xz.gro -box 8.04542 8.04542 10.19156

I've obtained the system with the broadered water layers again ( as in
the picture which I've shown).


My advice is still the same - you need box vectors that are compatible
with
both
a sensible water layer and membrane leaflets.

-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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University of Southampton, UK.
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[gmx-users] equilibrium for box of simulation

Dear GROMACS Users,

I asked this question before but I don't understand it!


I placed several materials in my box of simulation for example box with 
6nm*6nm*6nm and my materials are not placed in the smaller box but when I 
equilibrate my system, the box became smaller and temperature and pressure also 
equilibrate. my question is: is my system and equilibrate mistake, because of 
reach to smaller box? Is there equilibriums with reach to smaller box?


I thanks from you for help to me.
Best Regards
Sara

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RE: [gmx-users] Error with grompp


Hello everyone,
Justin, I have repeated the procedures without doing any changes and it does 
seem that you were right about the broken file. However now I get a different 
set of errors:
(1) ERROR 1 [file ffoplsaabon.itp, line 2692]:  Incorrect number of atomtypes 
for dihedral (4 instead of 2 or 4)



(2) ERROR 2 [file ffoplsaabon.itp, line 2694]:  Not enough parameters
and then a lot of errors of the type:

ERROR 3 [file S54.top, line 118]:  No default Bond types

ERROR 4 [file S54.top, line 120]:  No default Bond types

ERROR 5 [file S54.top, line 124]:  No default Bond types

ERROR 6 [file S54.top, line 127]:  No default Bond types...
Maybe the main question is for the third error is how to define these bond 
types and angles?
Thank you.

Elie


 Date: Wed, 3 Oct 2012 22:09:02 -0400
 From: jalem...@vt.edu
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] Error with grompp
 
 
 
 On 10/3/12 7:48 PM, Elie M wrote:
 
  Sorry it seems that those breaks are due to hotmail and not present in the 
  topology. Thanks for your reply. I still have problems...I will tell u 
  briefly and as clear as possible what i did.
  (1)  My top file has the following lines ate first:
  ; Include forcefield parameters   #include ffoplsaamod.itp[ moleculetype ]
  which means that when grompp is reading it, it will first go to 
  ffoplsaamod.itp.
  (2) After the description of what the ffoplsaamod is (commented by ;), 
  the input is simply:
  [ defaults ];nbfunc comb-rule   gen-pairs   fudgeLJ fudgeQQ1
  3   yes 0.5 0.5
  #include ffoplsaanb.itp#include ffoplsaabon.itp
  where the nonbonded and bonded parameters are included in this order (which 
  you have also mentioned in your previous e-mail). If i run grompp in this 
  way I get the error:
  Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line 
  read:'\par'Found a second defaults directive.
  which I really cannot understand. The above [defaults] is the first thing 
  that the code will pass through. How come it mentions this as a second 
  directory?
  (3) i commented the above [ defaults] with a ; and I get another error:
  Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ 
  atomtypes ]'Invalid order for directive atomtypes
  which might mean according to what I have read (correct me if I am wrong 
  please), that the order might be violated and that [atomtypes] should not 
  come first; but it is the first directive in the ffoplsaanb.itp file, which 
  should be read first.
  So what might be happening? what is going wrong? or maybe what am I 
  missing?Thank you all once again for the effort you are making in this forum
 
 
 It seems like the format of whatever files you're using is horribly broken.  
 I 
 would recommend starting over and not making any adjustments to any files 
 (removing lines, changing contents, adding comments, etc) unless you know 
 exactly what you're doing.  For example, the presence of '\par' in 
 ffoplsaamod.itp suggests wrong line endings (i.e. from not using a plain text 
 editor).
 
 -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] equilibrium for box of simulation


On 5/10/2012 12:06 AM, mohammad agha wrote:

Dear GROMACS Users,

I asked this question before but I don't understand it!


I placed several materials in my box of simulation for example box with 
6nm*6nm*6nm and my materials are not placed in the smaller box but when I 
equilibrate my system, the box became smaller and temperature and pressure also 
equilibrate. my question is: is my system and equilibrate mistake, because of 
reach to smaller box? Is there equilibriums with reach to smaller box?


At least one of your volume, contents or model physics are not 
consistent with the others, but only you can say which.


Mark
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Re: [gmx-users] Interaction study for peptide-receptor..




On 10/4/12 9:16 AM, rama david wrote:

Thank you  for reply,
  I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the  receptor binding site and used the the solid support
to the binding site and did simulation.
So if I freeze  the group is it will ok ??


I've already stated my opinion on this matter, so I won't state it again.

I will not try to pre-judge a study I have not read (regarding the solid 
support) but it seems to me that if you are analyzing the binding of a peptide 
to a protein, that is fairly straightforward MD without anything fancy.



Is it possible in gromacs to fix the residue on solid immobilized surface.
If it is how to do it??



Build a surface, create a merged moleculetype, and define bonds between protein 
atoms and surface atoms.  This all sounds like a ridiculous amount of work.



my question is How to decide which group are remove and which group should
keep in simulation.



IMHO, it's not worth doing in this way.

-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] equilibrium for box of simulation




On 10/4/12 10:06 AM, mohammad agha wrote:

Dear GROMACS Users,

I asked this question before but I don't understand it!


I placed several materials in my box of simulation for example box with 
6nm*6nm*6nm and my materials are not placed in the smaller box but when I 
equilibrate my system, the box became smaller and temperature and pressure also 
equilibrate. my question is: is my system and equilibrate mistake, because of 
reach to smaller box? Is there equilibriums with reach to smaller box?




What do you mean by my materials are not placed in the smaller box?

If a box compresses, it is because the initial configuration was incompatible 
with the desired equilibration conditions and it contracted produce the desired 
quantity (likely pressure).


-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] Error with grompp




On 10/4/12 10:12 AM, Elie M wrote:


Hello everyone,
Justin, I have repeated the procedures without doing any changes and it does 
seem that you were right about the broken file. However now I get a different 
set of errors:
(1) ERROR 1 [file ffoplsaabon.itp, line 2692]:  Incorrect number of atomtypes 
for dihedral (4 instead of 2 or 4)



(2) ERROR 2 [file ffoplsaabon.itp, line 2694]:  Not enough parameters


You should inspect ffoplsaabon.itp to see what is on these lines.  It is odd 
that grompp would complain about standard force field files if they have not 
been changed.



and then a lot of errors of the type:

ERROR 3 [file S54.top, line 118]:  No default Bond types

ERROR 4 [file S54.top, line 120]:  No default Bond types

ERROR 5 [file S54.top, line 124]:  No default Bond types

ERROR 6 [file S54.top, line 127]:  No default Bond types...
Maybe the main question is for the third error is how to define these bond 
types and angles?


If a certain interaction is not available in ffbonded.itp (i.e. you've got bonds 
that are not parameterized in the chosen force field) you need to add them 
either in ffbonded.itp (potentially dangerous, given the previous posts) or 
directly in the topology (probably safer).


-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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[gmx-users] equilibrium for box of simulation

Dear Justin,

my materials are not placed in the smaller box means if I select box with 
dimensions 5.99 nm, space is low and insufficient for my molecules! but after 
equilibrate the box become small.
According what you said, when the box become smaller in equilibrium, there is 
not mistake and it is natural?

Best Regards
Sara



- Forwarded Message -
From: Justin Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org
Cc: 
Sent: Thursday, October 4, 2012 5:52 PM
Subject: Re: [gmx-users] equilibrium for box of simulation



On 10/4/12 10:06 AM, mohammad agha wrote:
 Dear GROMACS Users,

 I asked this question before but I don't understand it!


 I placed several materials in my box of simulation for example box with 
 6nm*6nm*6nm and my materials are not placed in the smaller box but when I 
 equilibrate my system, the box became smaller and temperature and pressure 
 also equilibrate. my question is: is my system and equilibrate mistake, 
 because of reach to smaller box? Is there equilibriums with reach to smaller 
 box?



What do you mean by my materials are not placed in the smaller box?

If a box compresses, it is because the initial configuration was incompatible 
with the desired equilibration conditions and it contracted produce the desired 
quantity (likely pressure).

-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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[gmx-users] equilibrium for box of simulation

Dear Mark,

So, when in the equilibrium stage, the box become small, there is one mistake 
in my system?
I don't know where is my mistake!

Best Regards
Sara 




- Original Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc: 
Sent: Thursday, October 4, 2012 5:48 PM
Subject: Re: [gmx-users] equilibrium for box of simulation

On 5/10/2012 12:06 AM, mohammad agha wrote:
 Dear GROMACS Users,

 I asked this question before but I don't understand it!


 I placed several materials in my box of simulation for example box with 
 6nm*6nm*6nm and my materials are not placed in the smaller box but when I 
 equilibrate my system, the box became smaller and temperature and pressure 
 also equilibrate. my question is: is my system and equilibrate mistake, 
 because of reach to smaller box? Is there equilibriums with reach to smaller 
 box?

At least one of your volume, contents or model physics are not 
consistent with the others, but only you can say which.

Mark
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Re: [gmx-users] equilibrium for box of simulation




On 10/4/12 10:38 AM, mohammad agha wrote:

Dear Justin,

my materials are not placed in the smaller box means if I select box with 
dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate 
the box become small.


Please define what you mean here.  You start with a 6-nm cubic box.  How small 
does it get?  Are the box vectors trending downward, or do they converge?  What 
is the change in density, and is it acceptable?



According what you said, when the box become smaller in equilibrium, there is 
not mistake and it is natural?



That depends on the magnitude of the change.  Compression indicates that the 
pressure (and thus density of the system) was not at the desired value and the 
system is contracting.  The manner in which the contraction occurs (magnitude, 
speed) is the deciding factor as to whether or not there is a problem.


-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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[gmx-users] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)

2012-10-04 Thread jiang

Justin Lemkul wrote
On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:
Hi Justin,

I used ~20 windows to sample ~2 nm pulling. I notice that the distance
between the complex being increased during the pulling but not gradually.
At the distance of 0-1nm, there are 70 snapshots (the distance sometime
increased sometimes decreased). At the distance of 1-2nm, there are only
30 snapshots (the distance kept increasing always). At the distance more
than 3nm, the distance increased as 0.3nm of each snapshot, is it normal
and reliable?

I will assume you are using a harmonic potential (umbrella) to do the
pulling.
In this case, your observations are totally normal. When two species
interact
strongly, it is harder to pull them apart, thus the spring extends further
to
induce a larger force before displacement occurs. As the restoring forces
are
overcome, it is easier to move the pulled group through solution, so it
makes
more steady progress as the molecules are separated.

Hi Justin, it is right I am using umbrella pulling. Now here is another
hurdle in front of me: How to select the snapshots for umbrella samples?
Since the distance between two groups went higher or lower at the beginning
of the pulling. For example, during the pulling simulation, the distance
changes like:
0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44
0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) .
I suppose it doesn't matter which snapshots to be chosen, as long as the
snapshots can indicate a good spacing, the PMF result always should be same,
right?

Thanks, jiang.

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Re: [gmx-users] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)




On 10/4/12 10:52 AM, jiang wrote:

Justin Lemkul wrote

On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:

Hi Justin,

I used ~20 windows to sample ~2 nm pulling. I notice that the distance
between the complex being increased during the pulling but not gradually.
At the distance of 0-1nm, there are 70 snapshots (the distance sometime
increased sometimes decreased). At the distance of 1-2nm, there are only
30 snapshots (the distance kept increasing always). At the distance more
than 3nm, the distance increased as 0.3nm of each snapshot, is it normal
and reliable?



I will assume you are using a harmonic potential (umbrella) to do the
pulling.
In this case, your observations are totally normal.  When two species
interact
strongly, it is harder to pull them apart, thus the spring extends further
to
induce a larger force before displacement occurs.  As the restoring forces
are
overcome, it is easier to move the pulled group through solution, so it
makes
more steady progress as the molecules are separated.



Hi Justin, it is right I am using umbrella pulling. Now here is another
hurdle in front of me: How to select the snapshots for umbrella samples?
Since the distance between two groups went higher or lower at the beginning
of the pulling. For example, during the pulling simulation, the distance
changes like:
0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44
0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) .
I suppose it doesn't matter which snapshots to be chosen, as long as the
snapshots can indicate a good spacing, the PMF result always should be same,
right?



You need reasonable spacing and sufficient sampling in each window to allow for 
proper overlap of the umbrella potentials.


-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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[gmx-users] RE: Re: Binding Energy to Binding affinity (Kd)

2012-10-04 Thread Thomas Schlesier

You could use 'constraint' pull-mode instead of the 'umbrella' mode. 
Than the distance would change gradually and you won't observe the 
fluctuations in the distance.


greetings
thomas


Am 04.10.2012 16:58, schrieb gmx-users-requ...@gromacs.org:

On 10/4/12 10:52 AM, jiang wrote:

Justin Lemkul wrote

On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:

Hi Justin,

I used ~20 windows to sample ~2 nm pulling. I notice that the distance
between the complex being increased during the pulling but not gradually.
At the distance of 0-1nm, there are 70 snapshots (the distance sometime
increased sometimes decreased). At the distance of 1-2nm, there are only
30 snapshots (the distance kept increasing always). At the distance more
than 3nm, the distance increased as 0.3nm of each snapshot, is it normal
and reliable?



I will assume you are using a harmonic potential (umbrella) to do the
pulling.
In this case, your observations are totally normal.  When two species
interact
strongly, it is harder to pull them apart, thus the spring extends further
to
induce a larger force before displacement occurs.  As the restoring forces
are
overcome, it is easier to move the pulled group through solution, so it
makes
more steady progress as the molecules are separated.



Hi Justin, it is right I am using umbrella pulling. Now here is another
hurdle in front of me: How to select the snapshots for umbrella samples?
Since the distance between two groups went higher or lower at the beginning
of the pulling. For example, during the pulling simulation, the distance
changes like:
0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44
0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) .
I suppose it doesn't matter which snapshots to be chosen, as long as the
snapshots can indicate a good spacing, the PMF result always should be same,
right?


You need reasonable spacing and sufficient sampling in each window to allow for
proper overlap of the umbrella potentials.

-Justin


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[gmx-users] Re: equilibrium for box of simulation



Please keep the discussion on the gmx-users list.

On 10/4/12 11:28 AM, mohammad agha wrote:

Dear Justin,

Thank you very much from your help.
I don't know about vectors trending downward, or do they converge


You can plot box vectors from the .edr file.  That will give you their values 
and show trends in the data.



The change of density is from 1274 to 1685. and the slope of increasing the 
density at the first is much and then it become almost fix.



This outcome suggests that your box likely has stabilized.  You should still 
plot the vectors to understand what's going on.  You also need to assess whether 
or not this density is acceptable as an evaluation of your physical model of the 
system.


-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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[gmx-users] Re: vmd-l: Re: compiling VMD with gcc 4.7

2012-10-04 Thread lloyd riggs


Dear All,

I spent two days converting a .top file from gromos53a6 to one readable by 
VMD/NAMD.

Now I am about to begin the ffbonded/nonbonded to a readable format for the 
same and would like to know beforehand if anyone has already done this so I can 
just use the library?  Most are straightforward conversions of format.  The 
main prblem is the NAMD (I believe) does not already have the parameters for cg 
or merged CH croups.  The gromos force fields for gromacs only do this with 
chain non-polar, leaving the charged H groups alone.  I did find however, no 
equivalent with trying to first generate a .psf file, and then looking at the 
vdw /angle, dihedrals and non bonded files for NAMD.

Example a methyl is CH3 with a mass of 15.00 CH2 Mass 14 ,etc  with only 3 atom 
type changes, you would think it wouldnt be so painfull, but it turns into a 
hellish nightmare.

Any links or pointers would be appreciated, however I already assume I have to 
do this myself to use the VMD tools with Gromacs traj.  Its still shorter than 
3 months of simulations with a new index file.

Sincerely,

Stephan Watkins
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[gmx-users] Regarding g_covar

2012-10-04 Thread R.Vidya Rajendran (10PHD013)

Hello Everybody,

I am using g_covar with -xpmc flag in-oder to generate matrix of
atomic correlation coefficients. At present I am using g_covar script
given by Ran, which I downloaded from gromacs user modified script
pool.

Since Ran's script is for gromacs 3.3.3 and it not accept .trp input
from upgraded version (eg 4.5.5).

Anybody have upgraded g_covar which can do the same job.


regards
Vidya
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RE: [gmx-users] Error with grompp


Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; 
I have commented ; one line which was given the first two errors. Now the 
only errors remaining are the bonds, angles and some others. How to correct 
these?
For example one of them is (the error occuring at line 118 which is no 
different from others).
 111  [ bonds ]   112  ;  aiaj functc0c1
c2c3   113  1 2 1   114  1 5 1   115  1 
   47 1   116  2 3 1   117  248 1   118  3 
4 1
 How can the source of error be known and corrected?
Elie
 Date: Thu, 4 Oct 2012 10:26:04 -0400
 From: jalem...@vt.edu
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] Error with grompp
 
 
 
 On 10/4/12 10:12 AM, Elie M wrote:
 
  Hello everyone,
  Justin, I have repeated the procedures without doing any changes and it 
  does seem that you were right about the broken file. However now I get a 
  different set of errors:
  (1) ERROR 1 [file ffoplsaabon.itp, line 2692]:  Incorrect number of 
  atomtypes for dihedral (4 instead of 2 or 4)
 
 
 
  (2) ERROR 2 [file ffoplsaabon.itp, line 2694]:  Not enough parameters
 
 You should inspect ffoplsaabon.itp to see what is on these lines.  It is odd 
 that grompp would complain about standard force field files if they have not 
 been changed.
 
  and then a lot of errors of the type:
 
  ERROR 3 [file S54.top, line 118]:  No default Bond types
 
  ERROR 4 [file S54.top, line 120]:  No default Bond types
 
  ERROR 5 [file S54.top, line 124]:  No default Bond types
 
  ERROR 6 [file S54.top, line 127]:  No default Bond types...
  Maybe the main question is for the third error is how to define these bond 
  types and angles?
 
 If a certain interaction is not available in ffbonded.itp (i.e. you've got 
 bonds 
 that are not parameterized in the chosen force field) you need to add them 
 either in ffbonded.itp (potentially dangerous, given the previous posts) or 
 directly in the topology (probably safer).
 
 -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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[gmx-users] equilibrium for box of simulation

Dear Justin,

Thank you very much from your help.

Oh, yes, the vectors of box are downward in the first with much slope and then 
the slope became milder and milder and then it become almost fix.

For checking of density, should I use from formula: d=m/v?

Best Regards
Sara



- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org
Cc: 
Sent: Thursday, October 4, 2012 7:01 PM
Subject: Re: equilibrium for box of simulation


Please keep the discussion on the gmx-users list.

On 10/4/12 11:28 AM, mohammad agha wrote:
 Dear Justin,
 
 Thank you very much from your help.
 I don't know about vectors trending downward, or do they converge

You can plot box vectors from the .edr file.  That will give you their values 
and show trends in the data.

 The change of density is from 1274 to 1685. and the slope of increasing the 
 density at the first is much and then it become almost fix.
 

This outcome suggests that your box likely has stabilized.  You should still 
plot the vectors to understand what's going on.  You also need to assess 
whether or not this density is acceptable as an evaluation of your physical 
model of the system.

-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] Error with grompp




On 10/4/12 12:13 PM, Elie M wrote:


Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have 
commented ; one line which was given the first two errors. Now the only 
errors remaining are the bonds, angles and some others. How to correct these?
For example one of them is (the error occuring at line 118 which is no 
different from others).
  111  [ bonds ]   112  ;  aiaj functc0c1   
 c2c3   113  1 2 1   114  1 5 1   115  
147 1   116  2 3 1   117  248 1   118  3
 4 1
  How can the source of error be known and corrected?


The error message means that no suitable parameters exist in the force field for 
the bond that occurs between those atoms.  You either need to parameterize the 
problematic bond(s) yourself or obtain parameters from some other reliable source.


-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] equilibrium for box of simulation




On 10/4/12 12:25 PM, mohammad agha wrote:

Dear Justin,

Thank you very much from your help.

Oh, yes, the vectors of box are downward in the first with much slope and then 
the slope became milder and milder and then it become almost fix.

For checking of density, should I use from formula: d=m/v?



You already have the density value; you posted it before.

-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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[gmx-users] About Lipid Protein simualtion

2012-10-04 Thread vidhya sankar

Dear Justin ,
 Thank you for you Previous reply.  


I am doing  Simulation of Cyclic Peptide in Lipids  I am following your 
tutorial  When I use inflategro script For my System I have got Output 
System_inflated.gro file with certain message in Command prompt as follows  . 
The Below Message Shows That There is No Lipid Molecules Are Deleted  Should I 
Change the Cut-off or scaling Factor  to Delete the Lipid Molecules or is it 
enough ,  I Mean  Must Some Lipid Molecules Need to be Deleted ?


There are 128 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet 
Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...
Writing scaled bilayer  centered protein...
Calculating Area per lipid...
Protein X-min/max: 19    40
Protein Y-min/max: 21    39
X-range: 21 A    Y-range: 18 A
Building 21 X 18 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 4 nm^2
Area per lipid: 8.9375 nm^2
Area per protein, upper half: 3.5 nm^2
Area per lipid, upper leaflet : 8.9453125 nm^2
Area per protein, lower half: 3.5 nm^2
Area per lipid, lower leaflet : 8.9453125 nm^2
Writing Area per lipid...
Done!

2) Also When I Run Grompp for EM Which Topology Should  I use ?  I have  used 
my Multi chain     protein.top When I Have used that I got Error AS follows
Fatal error:

[ file strong_porse.itp, line 8 ]:
Atom index (4) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section 
position_restraints
in a part belonging to a different molecule than you intended to.
In that case move the position_restraints section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS

How to Rectify the Problem?


Thanks In Advance 

With High Regards 

S.Vidhyasankar
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Re: [gmx-users] About Lipid Protein simualtion

On 10/4/12 1:12 PM, vidhya sankar wrote:

Dear Justin ,
Thank you for you Previous reply.

I am doing Simulation of Cyclic Peptide in Lipids I am following your
tutorial When I use inflategro script For my System I have got Output
System_inflated.gro file with certain message in Command prompt as follows .
The Below Message Shows That There is No Lipid Molecules Are Deleted Should I
Change the Cut-off or scaling Factor to Delete the Lipid Molecules or is it
enough , I Mean Must Some Lipid Molecules Need to be Deleted ?

It would be highly unusual if no lipids were deleted, unless the protein is not
actually embedded in the membrane.

There are 128 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet
Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...
Writing scaled bilayer centered protein...
Calculating Area per lipid...
Protein X-min/max: 1940
Protein Y-min/max: 2139
X-range: 21 AY-range: 18 A
Building 21 X 18 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 4 nm^2
Area per lipid: 8.9375 nm^2
Area per protein, upper half: 3.5 nm^2
Area per lipid, upper leaflet : 8.9453125 nm^2
Area per protein, lower half: 3.5 nm^2
Area per lipid, lower leaflet : 8.9453125 nm^2
Writing Area per lipid...
Done!

2) Also When I Run Grompp for EM Which Topology Should I use ? I have used
my Multi chain protein.top When I Have used that I got Error AS follows
Fatal error:

[ file strong_porse.itp, line 8 ]:
Atom index (4) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section
position_restraints
in a part belonging to a different molecule than you intended to.
In that case move the position_restraints section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS

How to Rectify the Problem?

Position restraints can only be applied within a given [moleculetype]. Note
that the error is explained on the Gromacs website, along with an example of
proper usage:

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-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] Error with grompp


I guess now I get what is happening finally. Correct me if I am wrong.  The 
.top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was 
also modified to include atoms that were not there *but present in 
atomtypes.atp). The .top file describes all the bonds and angles in the 
molecule. This was successful. However the characteristics of some of those 
bonds are not described in the foplssabon.itp file; for example I have Sulfur 
in my molecule connected to carbon which has no entry in foplsaabon.itp and 
must be added to that file manually. I guess now I am in a position to check 
those bonds and add the relevant information which i will gather maybe from 
HYPERCHEM or ARGUSLAB??A final question is in order here:
what do the parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) 
represent and in what units?

Thank you very much
Elie  

 Date: Thu, 4 Oct 2012 12:25:48 -0400
 From: jalem...@vt.edu
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] Error with grompp
 
 
 
 On 10/4/12 12:13 PM, Elie M wrote:
 
  Thanks a lot. I have sorted out the error that occured in the 
  ffoplsaabon.itp; I have commented ; one line which was given the first 
  two errors. Now the only errors remaining are the bonds, angles and some 
  others. How to correct these?
  For example one of them is (the error occuring at line 118 which is no 
  different from others).
111  [ bonds ]   112  ;  aiaj functc0c1   
   c2c3   113  1 2 1   114  1 5 1   
  115  147 1   116  2 3 1   117  248 1   
  118  3 4 1
How can the source of error be known and corrected?
 
 The error message means that no suitable parameters exist in the force field 
 for 
 the bond that occurs between those atoms.  You either need to parameterize 
 the 
 problematic bond(s) yourself or obtain parameters from some other reliable 
 source.
 
 -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] Error with grompp




On 10/4/12 4:22 PM, Elie M wrote:


I guess now I get what is happening finally. Correct me if I am wrong.  The
.top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which
was also modified to include atoms that were not there *but present in
atomtypes.atp). The .top file describes all the bonds and angles in the
molecule. This was successful. However the characteristics of some of those
bonds are not described in the foplssabon.itp file; for example I have Sulfur
in my molecule connected to carbon which has no entry in foplsaabon.itp and
must be added to that file manually. I guess now I am in a position to check
those bonds and add the relevant information which i will gather maybe from
HYPERCHEM or ARGUSLAB??A final question is in order here: what do the


You will have to calculate reasonable values in some way, yes.


parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and
in what units?



All of this is in the manual.

-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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[gmx-users] Error There is no domain decomposition for 6 nodes that is compatible

2012-10-04 Thread Sonia Aguilera

Hi,

I am performing a free energy calculation based on Justin Lemkul's tutorial.
My system is a protein in water and dodecane and I'm coupling the protein
considering none to only vdw interactions for my lambda 0 and 1 states.
However, I get this error when trying to minimize the system:

Fatal error:
There is no domain decomposition for 6 nodes that is compatible with the
given box and a minimum cell size of 7.55833 nm min1.0.mdp
http://gromacs.5086.n6.nabble.com/file/n5001648/min1.0.mdp
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition

I know I can fix easily this problem by using -nt 1 option. But I still want
to use all available cores. I suspect the error is in the mdp file because
if I use the following mdp file for the minimization it works.

title = cpeptide
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002; ps !
nsteps = 1000
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb= 1.0
rvdw= 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01

Obviously this mdp file does not work for free energy calculations. I still
want to use the attached one, but I don´t know what to change to make it
work.

This is the link for my log and mdp file.
mdp_and_log_files.zip
http://gromacs.5086.n6.nabble.com/file/n5001648/mdp_and_log_files.zip

Thank you in advance,

Sonia Aguilera
Graduate Assistant
Universidad de los Andes-Colombia

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Re: [gmx-users] Error There is no domain decomposition for 6 nodes that is compatible

On 10/4/12 4:54 PM, Sonia Aguilera wrote:

Hi,

Obviously this mdp file does not work for free energy calculations. I still
want to use the attached one, but I don´t know what to change to make it
work.

This is the link for my log and mdp file.
mdp_and_log_files.zip
http://gromacs.5086.n6.nabble.com/file/n5001648/mdp_and_log_files.zip

The problem comes from these settings:

couple-moltype = Protein_chain_A ; name of moleculetype to decouple
couple-lambda0 = none ; turn off everything
couple-lambda1 = vdw ; only van der Waals interactions
couple-intramol = no

You're transforming the protein using long-range exclusions and pair
interactions (couple-intramol = no). These interactions make the required DD
cell size very large. Then you run into the fact that you can't decompose any
system into any arbitrary number of DD cells, because their size is limited by
the bonded interactions, pairs, cutoffs, and other factors.

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

-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: vmd-l: Re: compiling VMD with gcc 4.7


On 5/10/2012 1:49 AM, lloyd riggs wrote:

Please choose descriptive subjects and start new email messages when 
posting to mailing lists. This makes people better able to respond to 
you by allowing mail reading software to work properly. Cross-posting to 
the VMD and GROMACS lists when your question relates to conversion of 
file formats between GROMACS and NAMD seems a bit strange, too.



Dear All,

I spent two days converting a .top file from gromos53a6 to one readable by 
VMD/NAMD.

Now I am about to begin the ffbonded/nonbonded to a readable format for the 
same and would like to know beforehand if anyone has already done this so I can 
just use the library?  Most are straightforward conversions of format.  The 
main prblem is the NAMD (I believe) does not already have the parameters for cg 
or merged CH croups.  The gromos force fields for gromacs only do this with 
chain non-polar, leaving the charged H groups alone.  I did find however, no 
equivalent with trying to first generate a .psf file, and then looking at the 
vdw /angle, dihedrals and non bonded files for NAMD.

Example a methyl is CH3 with a mass of 15.00 CH2 Mass 14 ,etc  with only 3 atom 
type changes, you would think it wouldnt be so painfull, but it turns into a 
hellish nightmare.


I don't understand what the problem is from this description.


Any links or pointers would be appreciated, however I already assume I have to 
do this myself to use the VMD tools with Gromacs traj.  Its still shorter than 
3 months of simulations with a new index file.


VMD can just read a gromacs trajectory. What's the problem with that? 
Why do you (think you) need a matching .psf?


Mark
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Re: [gmx-users] Problem with the installation of Gromacs 4-5.5


On 4/10/2012 3:37 PM, Deepak Ojha wrote:

Dear All
I want to use Amber force field in Gromacs therefore I installed the
latest version of Gromacs and
installed accordingly as per as the instructions given in INSTALL.automake file.
./configure
make
make install

It works fine and shows the message that installation is complete but
none of the commands like
pdb2gmx,mdrun works.Even the luck does not works which is meant to
test the installation of gromacs.
What is the issue with the installation.Please help me resolve it.


http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation

Mark
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[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly.

2012-10-04 Thread Bao Kai

Hi, all,

I am still working on the molecular simulation of CO2 and H2O mixture.

The information of the molecules types and the force field model are
all defined in the a.top file.

  1 [ defaults ]
  2 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  3 1  3  yes 0.50.5
  4 [ atomtypes ]
  5 ;   type  at.nummasschargeptypesigmaepsilon
  6   CO   6 12.01100.5888A   0.27918   0.2398
  7   OC   8 15.9994   -0.2944A   0.3   0.6872
  8   OW   6 15.99940   -0.8476A 0.316557 0.650194
  9   HW   1 1.008000.4238A  0.0   0.0
 10 [ moleculetype ]
 11 ;name nrexcl
 12 CO2 3
 13 [atoms]
 14 ;   nr   type  resnr residue  atom   cgnr charge   mass


 32 [moleculetype]
 33 ; molname nrexcl
 34 SOL 2
 35 [atoms]
 36 ;   nr   type  resnr residue  atom   cgnr charge   mass
...
 47 [system]
 48 sparkling water
 49 [molecules]
 50 CO2 100
 51 SOL  3000

I create on co2.gro file to put one CO2 molecule inside.

Then I used

genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top

to put 190 CO2 molecules inside the box.

Then I used
genbox -cp a.gro -o b.gro -box 7  -cs -maxsol 9810 -p a.top

to put 9810 H2O molecules inside the box.

In the file a.top, the No. of the H2O was updated correctly, while the
No. of the CO2 molecules was not updated.   The No. of the atoms in
.gro files are correct.

Can you please tell me the reason or how to solve it?

Thank you very much.

Best Retards,
Kai
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Re: [gmx-users] The No. of the CO2 melecules in top file can not be updated correctly.




On 10/4/12 5:29 PM, Bao Kai wrote:

Hi, all,

I am still working on the molecular simulation of CO2 and H2O mixture.

The information of the molecules types and the force field model are
all defined in the a.top file.

   1 [ defaults ]
   2 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
   3 1  3  yes 0.50.5
   4 [ atomtypes ]
   5 ;   type  at.nummasschargeptypesigmaepsilon
   6   CO   6 12.01100.5888A   0.27918   0.2398
   7   OC   8 15.9994   -0.2944A   0.3   0.6872
   8   OW   6 15.99940   -0.8476A 0.316557 0.650194
   9   HW   1 1.008000.4238A  0.0   0.0
  10 [ moleculetype ]
  11 ;name nrexcl
  12 CO2 3
  13 [atoms]
  14 ;   nr   type  resnr residue  atom   cgnr charge   mass


  32 [moleculetype]
  33 ; molname nrexcl
  34 SOL 2
  35 [atoms]
  36 ;   nr   type  resnr residue  atom   cgnr charge   mass
...
  47 [system]
  48 sparkling water
  49 [molecules]
  50 CO2 100
  51 SOL  3000

I create on co2.gro file to put one CO2 molecule inside.

Then I used

genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top

to put 190 CO2 molecules inside the box.

Then I used
genbox -cp a.gro -o b.gro -box 7  -cs -maxsol 9810 -p a.top

to put 9810 H2O molecules inside the box.

In the file a.top, the No. of the H2O was updated correctly, while the
No. of the CO2 molecules was not updated.   The No. of the atoms in
.gro files are correct.

Can you please tell me the reason or how to solve it?



genbox only updates water molecules in the topology.  Anything else is up to 
you.  Beware that a linear, 3-atom model of CO2 is probably not going to work 
due to issues with linear angles, as has been discussed frequently on the list. 
 A more robust approach involves virtual sites.


-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] Error with grompp

I guess the first parameter of each pair is easy to find. what about kb? k 
theta?. kb is the force constant isnt it? any reference about a method how 
to calculate them please? pr anything atht might be of help.

Elie

 Date: Thu, 4 Oct 2012 16:25:35 -0400
 From: jalem...@vt.edu
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] Error with grompp

 On 10/4/12 4:22 PM, Elie M wrote:

  I guess now I get what is happening finally. Correct me if I am wrong.  The
  .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which
  was also modified to include atoms that were not there *but present in
  atomtypes.atp). The .top file describes all the bonds and angles in the
  molecule. This was successful. However the characteristics of some of those
  bonds are not described in the foplssabon.itp file; for example I have 
  Sulfur
  in my molecule connected to carbon which has no entry in foplsaabon.itp and
  must be added to that file manually. I guess now I am in a position to check
  those bonds and add the relevant information which i will gather maybe from
  HYPERCHEM or ARGUSLAB??A final question is in order here: what do the

 You will have to calculate reasonable values in some way, yes.

  parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and
  in what units?

 All of this is in the manual.

 -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] Error with grompp




On 10/4/12 5:56 PM, Elie M wrote:


I guess the first parameter of each pair is easy to find. what about kb? k 
theta?. kb is the force constant isnt it? any reference about a method how 
to calculate them please? pr anything atht might be of help.



Bonded parameters are generally based on vibrational spectra and X-ray data. 
For OPLS, the bonded parameters were originally taken from an AMBER parameter 
set in the mid-1980's and have some terms have subsequently been revised over time.


-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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[gmx-users] equilibrium for box of simulation