[gmx-users] setting working directory

[Efrat Exlrod]

Hi There!



Is it possible to run mdrun from a shared directory and set the working 
directory to a local directory on the computer on which it runs, in order to 
decrease NFS load?



Thanks, Efrat
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Re: [gmx-users] setting working directory

[Mark Abraham]

On 1/11/2011 6:33 PM, Efrat Exlrod wrote:


Hi There!

Is it possible to run mdrun from a shared directory and set the 
working directory to a local directory on the computer on which it 
runs, in order to decrease NFS load?





/path/to/shared/mdrun -deffnm /path/to/local/my_simulation

Mark
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[gmx-users] Kinetic Energy in FEP calculations

[Connie Wang]

Hello,

 I'm attempting to calculate a relative free energy of hydration between
Argon and Neon. However when perturbing from Argon(aq)->Neon(aq) I was
surprised to compute a change in free energy of 1.2kJ/mol, where the
literature values suggest that the hydration energy of Argon is ~-9kJ/mol
and neon is ~-8kJ/mol, which means that I should have seen a change in free
energy of ~-1kJ/mol.

 Interestingly, I noticed that this 2kJ/mol difference could be resolved if
I subtract the dEkin/dlambda value obtained from the edr file. A clumsy
look into the source code seemed to confirm that there is a dEkin/dlambda
term included in the dH/dlambda calculation which results from the change
in mass during the mutation.  However it seems in the literature that most
people calculate the free energy between two states as the difference of
the configurational partition functions, and thus should be a function of
the positions and independent of the mass.

It seems tempting to me to resolve my problem by simply subtracting off the
dEkin/dlambda term, since I am in the NPT ensemble (and at constant
temperature the Ekin shouldn't change). Does this seem reasonable? Is there
a good reason for including this dEkin/dlambda term in FEP calculations? If
I'm interested only in the difference between the configurational partition
functions in the NPT ensemble, should the dEkin/dlambda term be included in
the first place?



In case it helps, my topology file and mdp file:

*Topology File*
; Argon parameters from Maitland, G. C.; Rigby, M.; Smith, E. B.; Wakeham,
W. A.
;Intermolecular Forces: Their Origin and Determination;

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.01.0

[ atomtypes ]
  ArAr  39.948 0.000A 3.41000e-01   9.96000e-01
  NeNe  20.180 0.000A 2.72000e-01   3.91000e-01
  DNe   DNe 20.180 0.000A 0.0e-01   0.0e-01
  DAr   DAr 39.948 0.000A 0.0e-01   0.0e-01

; Include water topology
[ atomtypes ]
OW  OW 16.00   0.  A   3.15061e-01  6.36386e-01
HW  HW 1.008   0.  A   0.0e+00  0.0e+00
[ moleculetype ]
; molname   nrexcl
SOL 1

[ atoms ]
; id  at type res nr  res name  at name  cg nr  chargemass
  1   OW  1   SOL   OW   1  -0.83416.0
  2   HW  1   SOL   HW1  1   0.417 1.00800
  3   HW  1   SOL   HW2  1   0.417 1.00800

[ settles ]
; i j   funct   length
1   1   0.09572 0.15139

[ exclusions ]
1   2   3
2   1   3
3   1   2


[ moleculetype ]
; Namenrexcl
 Argon   1

[ atoms ]
; residue   3 LEU rtp CLEU q -1.0
;   nr   type   resnr residue atom   cgnr   charge   masstypeB
chargeB massB
1 Ar  1Ar  Ar 1 0. 39.948Ne
 0.  20.180

[ system ]
; Name
Argon Mutate Neon

[ molecules ]
; Compound#mols
Argon   1
SOL215

*MDP File*
; Run control
integrator   = sd   ; Langevin dynamics
dt   = 0.002
nsteps   = 250  ; 5 ns

; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 0.9
; Electrostatics
coulombtype  = PME
rcoulomb = 0.9

; van der Waals
vdw-type = switch
rvdw-switch  = 0.7
rvdw = 0.8

; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres

; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.1
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no

; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 298

; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0

; Free energy control stuff
free_energy  = yes
init_lambda  = 0.0
delta_lambda = 0
foreign_lambda   = 0.05
sc-alpha = 0.5
sc-power = 1.0
sc-sigma = 0.3
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
lincs-order  = 12

I used 10 windows for the perturbation and ran each window for 3ns. The
results were then combined using the g_bar utility

Thanks!
-Connie
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Re: [gmx-users] Charmm27 ff for membrane protein simulation

[James Starlight]

It seems very strange but i could not find such parameters for charmm
lipids :( only berger lipids are presented on the world wide :D

I've another question about conversion of the topology formats

e.g I have topology and parameters for some molecules written for CHARMM
program in file .rtf and .prm file formats respectively
could I convert this topology  to the gromacs standart .rtp or .itp
topology ? How I could adapt parameters in .prm for gromacs ?


James

2011/10/19 James Starlight 

> Thomas, Justin thank you for that information
>
>
> Recently I've alredy tried to investigate CHARMM36 ff. I found that
> lipid.rtp of that ff consist of data for different DPP lipids. But in those
> DPPC lipid bilayer that I've used in the Justin's tutorial consist of 50
> atoms for each monomer. In contrary the DPP lipids in the CHARMM ff consist
> of more atoms and has another atom difinition.
>
> E.g If I've tried to load my dppc.pdb to the pdb2gmx I've obtained error
> that
> Residue 'DPP' not found in residue topology database
>
> Where I could find already preequilibrated bilayers adapted for the CHARMM
> ff?
>
>
> James
>
>
> 2011/10/18 Thomas Piggot 
>
>> By default in the CHARMM27 force field files there is no DPPC, as this is
>> made up from a combination of other entries in the rtp file (because this
>> is the way it is done in the CHARMM program's files). If you wish to use
>> DPPC you can construct yourself a complete DPPC rtp entry. To do this you
>> it is probably easiest to duplicate the DMPC entry and add the
>> corresponding atoms and bonds for two extra carbons in each tail.
>>
>> Alternatively you could use the CHARMM36 force field (available to
>> download from the contributions section of the website), there should
>> already be an entry for DPPC.
>>
>> Cheers
>>
>> Tom
>>
>>
>> On 18/10/11 19:45, Justin A. Lemkul wrote:
>>
>>>
>>> James Starlight wrote:
>>>
 Greetings!


 Recently I've found that Charmm27 ff is widely used for the simulation
 of the membrane proteins. I've tried to work with pure DPPC bilayer in
 pdb2grx and obtain that charm27 ff included in the Gromacs is lack for
 the parametries for the lipids.

 Could you tell me where I could obtain those parametries ( and tutorial
 of how it might be included in processing of lipids) or full functional
 charmm27 ff that already has pre-built those parametries?

  Most of the common lipids are already present in lipids.rtp in
>>> charmm27.ff in
>>> Gromacs 4.5.x; if you are looking for lipids not present there, please
>>> be more
>>> specific as to what you need.
>>>
>>> The only membrane protein tutorial to my knowledge is my own.  Dealing
>>> with
>>> CHARMM should be significantly easier, however, as no modification of
>>> the force
>>> field is necessary.  Run pdb2gmx on a single lipid molecule, convert the
>>> .top to
>>> .itp (see the wiki) and #include it in the .top for your protein, just
>>> like in
>>> my tutorial.
>>>
>>> -Justin
>>>
>>>  Thank you for help


 James


>> --
>> Dr Thomas Piggot
>> University of Southampton, UK.
>>
>>
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Re: [gmx-users] setting working directory

[lina]

On Tue, Nov 1, 2011 at 3:33 PM, Efrat Exlrod  wrote:
> Hi There!
>
>
>
> Is it possible to run mdrun from a shared directory and set the working
> directory to a local directory on the computer on which it runs, in order to
> decrease NFS load?

Yes. I attached a generic script, you can modify from it if you want.

##project set up by the user
GENERICNAME="Your_project_name"

## input data folder
INPUTDATAFOLDER=${HOME}/data


## cluster environment
 shared scratch folder
SCRATCH=${HOME}/globalscracth

 node local scratch folder
LOCALSCRATCH=${LOCALSCRATCH:-/scratch}/${USER}

## set up a unique tag suffix
JOBSUFFIX=$(date +%Y_%m_%d-%H_%M_%S-%N)-$$

## job name
JOBNAME=${GENERICNAME}-${JOBSUFFIX}


## share job working directory
JOBFOLDER=${SCRATCH}/${JOBNAME}
mkdir -p ${JOBFOLDER}

## local job working directory
LOCALJOBFOLDER=${LOCALSCRATCH}/${JOBNAME}
mkdir -p ${LOCALJOBFOLDER}

## let work on the local computer
cd ${LOCALJOBFOLDER}

## let transfert input data
cp -p ${INPUTDATAFOLDER}/*.data .

## let begin the job


## let transfert output data
mv outputdata.data ${JOBFOLDER}

## clean up the local scratch
cd ..
rm -rf ${JOBNAME}

## go home
cd

## exit
exit 0

##
## eos


>
>
>
> Thanks, Efrat
>
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[gmx-users] umbrella sampling convergence

[Vijayaraj]

Hello,

What is the criteria for umbrella sampling convergence. If I am right, the
pulling force and COM distance should be converged. I do not see force or
COM distance convergence after 10ns of simulation.

Regards,
Vijay
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[gmx-users] umbrella sampling convergence

[chris . neale]

The criteria are the same for any type of simulation. Generally, you  
must show that, as far as you can tell, the values that you derive are  
not going to change if you run the simulation a lot longer. Different  
quantities converge at different rates, so ideally you should check  
them all independently. In practice, people tend to pick one that they  
think will converge the most slowly and analyze the convergence of  
that. This could be your PMF.


If it's not converged then you can either run longer or figure out  
what is relaxing slowly and include that degree of freedom in your  
reaction coordinate.


Chris.

-- original message --

What is the criteria for umbrella sampling convergence. If I am right, the
pulling force and COM distance should be converged. I do not see force or
COM distance convergence after 10ns of simulation.

Regards,
Vijay

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Re: [gmx-users] Re: Structure preparation for the simulation

[James Starlight]

Itamar, thank you for advise but I dont like swith prot :))

Justin, what xleap prameter set have you used for KALP peptide? I want to
find parameters wich would not affect any problems in my further simulation
via gromos in Gromacs.


James



2011/10/31 Itamar Kass 

> Hi James,
>
> I usually use Swiss-PdbViewer (http://spdbv.vital-it.ch/disclaim.html).
> Despite being an old and not well supported for any system, it is still a
> free and easy to use and allows the building and mutating of residues  in
> addition to automatically adding missing atoms.
>
> You can just build an extra GLY at the end of the your chain and using
> text editor change it to N/C-caps.
>
>
> Cheers,
> Itamar
>
> On 31/10/2011, at 11:16 PM, Dr. Vitaly V. Chaban wrote:
>
> Dear Gromacs Users!
>
>
>
> I'd like to know about external software wich could be used for structure
>
> processing for the futher simulation in Gromacs. Today I've tried one of
> the
>
> most popular such software Amber tools but I've forced with problems during
>
> compilation of it ") So I'm looking for possible analogues )
>
>
> First of all I'm intresting in software for the addition different CAPing
>
> groups to N and C termi of my protein.
>
>
> Is there any plugins for Pymol or VMD for such purposes? I've loked for
> this
>
> option in both of that software but couldnot  find
>
>
>
> Thank you for your help,
>
>
> James
>
>
> Among free solutions... maybe this would help:
> http://www.chemaxon.com/marvin/sketch/index.php
>
> I don't know molecular editor plugins for VMD, but it would be cool,
> if one is accessible.
>
> --
> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
> Univ. Rochester, Rochester, New York 14627-0216
> THE UNITED STATES OF AMERICA
> --
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>
>
> --
>
> "In theory, there is no difference between theory and practice. But, in
> practice, there is." - Jan L.A. van de Snepscheut
>
> ===
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail:  itamar.k...@monash.edu
> 
>
>
>
>
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Re: [gmx-users] Re: Structure preparation for the simulation

[Justin A. Lemkul]

James Starlight wrote:

Itamar, thank you for advise but I dont like swith prot :))

Justin, what xleap prameter set have you used for KALP peptide? I want 
to find parameters wich would not affect any problems in my further 
simulation via gromos in Gromacs.





I only used xleap to build the caps.  Anything else was irrelevant.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Link to Intel MKL (fftw) via cmake options

[Szilárd Páll]

Thanks for the feeback!

I suspect that either something is simply broken in CMake 2.8.3 or it
has "feature" which somehow conflicts with the way the "install-mdrun"
custom target is implemented.

Anyway, I think we can consider this as a pretty much confirmed bug.
Would you mind entering it as a bug in redmine.gromacs.org. I'll look
into the issue in the coming days.

Cheers,
--
Szilárd



On Sat, Oct 29, 2011 at 11:56 PM, Mirco Wahab
 wrote:
> On 24.10.2011 23:23, Szilárd Páll wrote:
>>
>> I've just realized that both you and the similar report you linked to
>> were using CMake 2.8.3. If you don't succeed could you try another
>> CMake version?
>
> I could replicate the error with the simple cmake inviocation you proposed
> in your reply:
>
>> cmake ../gromacs-4.5.5 -DGMX_MPI=ON
>>  -DCMAKE_INSTALL_PREFIX=/tmp/gromacs-4.5 &&
>>    make mdrun -j4 &&  make install-mdrun
>
> This fails w/cmake 2.8.3 as before.
>
> Then, I installed cmake 2.8.6 on the same system, cleaned the
> build path and rerunned the build.
>
> Your suspicion was correct, *it now works* (w/2.8.6).
>
> So, 2.8.3 messes up the build process independend
> of the specific tool chain, maybe this could be
> added as a warning to the compilation instructions.
>
> BTW, I even managed to get an win64 (multithreaded,
> non-MPI) executeable displaying respectable performance
> by using  windows-cmake, visual studio 2010 SP1,
> visual studio sdk SP1 7.1/64, and Nasm-win.
>
> Thank you very much for your help.
>
> M.
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Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

[Szilárd Páll]

On Mon, Oct 31, 2011 at 1:06 PM, Mark Abraham  wrote:
> On 30/10/2011 8:56 AM, Mirco Wahab wrote:
>>
>> On 24.10.2011 23:23, Szilárd Páll wrote:
>>>
>>> I've just realized that both you and the similar report you linked to
>>> were using CMake 2.8.3. If you don't succeed could you try another
>>> CMake version?
>>
>> I could replicate the error with the simple cmake inviocation you proposed
>> in your reply:
>>
>>> cmake ../gromacs-4.5.5 -DGMX_MPI=ON
>>>  -DCMAKE_INSTALL_PREFIX=/tmp/gromacs-4.5 &&
>>>    make mdrun -j4 &&  make install-mdrun
>>
>> This fails w/cmake 2.8.3 as before.
>>
>> Then, I installed cmake 2.8.6 on the same system, cleaned the
>> build path and rerunned the build.
>>
>> Your suspicion was correct, *it now works* (w/2.8.6).
>>
>> So, 2.8.3 messes up the build process independend
>> of the specific tool chain, maybe this could be
>> added as a warning to the compilation instructions.
>
> Thanks for the report. We actually do have a warning against 2.8.3 here
> http://www.gromacs.org/Developer_Zone/Cmake but I don't know if it is the
> origin of your issue.

That bug is related to ASM compiler detection which should have
nothing to do with this issue.

--
Szilárd


> Mark
>
>>
>> BTW, I even managed to get an win64 (multithreaded,
>> non-MPI) executeable displaying respectable performance
>> by using  windows-cmake, visual studio 2010 SP1,
>> visual studio sdk SP1 7.1/64, and Nasm-win.
>>
>> Thank you very much for your help.
>>
>> M.
>
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[gmx-users] Justin Tutorial - Protein-Ligand

[Steven Neumann]

Dear Gmx Users, Dear Justin,

As I read in your tutorial you restrained the ligand during the
quilibration: NVT and NPT. My questions is: is it required?
Why cant we simply restrain the protein and let the ligand and water to
move around? Will there be a huge difference?

Thank you,

Steven
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Re: [gmx-users] Justin Tutorial - Protein-Ligand

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gmx Users, Dear Justin,
 
As I read in your tutorial you restrained the ligand during the 
quilibration: NVT and NPT. My questions is: is it required?
Why cant we simply restrain the protein and let the ligand and water to 
move around? Will there be a huge difference?
 


Do what suits your system best.  If the ligand position requires refinement, let 
it move during equilibration.  Maybe you might want to do it in steps - protein 
and ligand restrained, then just protein restrained, etc.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] PCA on secondary structure of protein.

[vivek modi]

Hi,

I plan to perform PCA on a globular protein which I am studying. The
simulation for the same is done for 100ns.
I have small doubt. Is it appropriate to perform PCA to study the movement
in protein on only secondary structure elements (helices in this case).
My protein contains long loops which do not play any role. Is it
appropriate to group only the helices together ignoring the loops and
perform PCA ?

Any help is appreciated.


Regards,

-Vivek Modi
Graduate Student
IITK.
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[gmx-users] Ligand topology in topol.top

[Steven Neumann]

Hi Guys,

I am using Charmm27 ff for my protein and ligand system. I used SwissParam
to generate the topology for my ligand. I included the obtained topology of
my ligand as in Justin tutorial:


; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Include ligand topology

#include "ligand.itp"

; Ligand position restraints

#ifdef POSRES

#include "posre_ligand.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"

When I wanted to run NVT I obtained:

Fatal error:
Syntax error - File egcg.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes


However when I included my topology as:


; Include forcefield parameters

#include "charmm27.ff/forcefield.itp"

#include "ligand.itp"

[ moleculetype ]

; Name nrexc

..

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Ligand position restraints

#ifdef POSRES

#include "posre_egcg.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"


Everything seems to be ok!
Any clue why is that?


Regards,

Steven
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Re: [gmx-users] Ligand topology in topol.top

[Justin A. Lemkul]

Steven Neumann wrote:

Hi Guys,
 
I am using Charmm27 ff for my protein and ligand system. I used 
SwissParam to generate the topology for my ligand. I included the 
obtained topology of my ligand as in Justin tutorial:
 


; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Include ligand topology

#include "ligand.itp"

; Ligand position restraints

#ifdef POSRES

#include "posre_ligand.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"

 
When I wanted to run NVT I obtained:
 
Fatal error:

Syntax error - File egcg.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
 
 
However when I included my topology as:
 


; Include forcefield parameters

#include "charmm27.ff/forcefield.itp"

#include "ligand.itp"

[ moleculetype ]

; Name nrexc

..

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Ligand position restraints

#ifdef POSRES

#include "posre_egcg.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"


 
Everything seems to be ok!

Any clue why is that?
 


The topology must follow a defined order.  Please consult Chapter 5 of the 
manual for the required hierarchy.  Of course, the latter case will also not 
work, because you've introduced ligand position restraints after the protein 
[moleculetype], so if invoked, they will cause a different fatal error.


The Gromacs site also has more on these types of errors, as well as the list 
archive, where this error has been posted and solved hundreds of times.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Hi

[X Rules]

gmx its about time people saw the value of the internet 
http://www.newsl3ireports.com/1/ see ya
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Re: [gmx-users] PCA on secondary structure of protein.

[Tsjerk Wassenaar]

Sure!

You'll just be looking at correlations between secondary structure
elements, disregarding the role that the loops may play. But it's a
sound approach.

:)

Tsjerk

On Tue, Nov 1, 2011 at 3:44 PM, vivek modi  wrote:
> Hi,
>
> I plan to perform PCA on a globular protein which I am studying. The
> simulation for the same is done for 100ns.
> I have small doubt. Is it appropriate to perform PCA to study the movement
> in protein on only secondary structure elements (helices in this case).
> My protein contains long loops which do not play any role. Is it appropriate
> to group only the helices together ignoring the loops and perform PCA ?
>
> Any help is appreciated.
>
>
> Regards,
>
> -Vivek Modi
> Graduate Student
> IITK.
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Ligand topology in topol.top

[Steven Neumann]

On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Hi Guys,
>>  I am using Charmm27 ff for my protein and ligand system. I used
>> SwissParam to generate the topology for my ligand. I included the obtained
>> topology of my ligand as in Justin tutorial:
>>
>> ; Include Position restraint file
>>
>> #ifdef POSRES
>>
>> #include "posre.itp"
>>
>> #endif
>>
>> ; Include ligand topology
>>
>> #include "ligand.itp"
>>
>> ; Ligand position restraints
>>
>> #ifdef POSRES
>>
>> #include "posre_ligand.itp"
>>
>> #endif
>>
>> ; Include water topology
>>
>> #include "charmm27.ff/tip3p.itp"
>>
>>  When I wanted to run NVT I obtained:
>>  Fatal error:
>> Syntax error - File egcg.itp, line 7
>> Last line read:
>> '[ atomtypes ] '
>> Invalid order for directive atomtypes
>>  However when I included my topology as:
>>
>> ; Include forcefield parameters
>>
>> #include "charmm27.ff/forcefield.itp"
>>
>> #include "ligand.itp"
>>
>> [ moleculetype ]
>>
>> ; Name nrexc
>>
>> ..
>>
>> ; Include Position restraint file
>>
>> #ifdef POSRES
>>
>> #include "posre.itp"
>>
>> #endif
>>
>> ; Ligand position restraints
>>
>> #ifdef POSRES
>>
>> #include "posre_egcg.itp"
>>
>> #endif
>>
>> ; Include water topology
>>
>> #include "charmm27.ff/tip3p.itp"
>>
>> 
>>  Everything seems to be ok!
>> Any clue why is that?
>>
>>
>
> The topology must follow a defined order.  Please consult Chapter 5 of the
> manual for the required hierarchy.  Of course, the latter case will also
> not work, because you've introduced ligand position restraints after the
> protein [moleculetype], so if invoked, they will cause a different fatal
> error.
>
> The Gromacs site also has more on these types of errors, as well as the
> list archive, where this error has been posted and solved hundreds of times.
>
> -Justin
>
> Thank you Justin! But actually the last case I provided actually works...


Steven
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Re: [gmx-users] Ligand topology in topol.top

[Justin A. Lemkul]

Steven Neumann wrote:



On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:

Hi Guys,
 I am using Charmm27 ff for my protein and ligand system. I used
SwissParam to generate the topology for my ligand. I included
the obtained topology of my ligand as in Justin tutorial:
 
; Include Position restraint file


#ifdef POSRES

#include "posre.itp"

#endif

; Include ligand topology

#include "ligand.itp"

; Ligand position restraints

#ifdef POSRES

#include "posre_ligand.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"

 When I wanted to run NVT I obtained:
 Fatal error:
Syntax error - File egcg.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
 However when I included my topology as:
 
; Include forcefield parameters


#include "charmm27.ff/forcefield.itp"

#include "ligand.itp"

[ moleculetype ]

; Name nrexc

..

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

; Ligand position restraints

#ifdef POSRES

#include "posre_egcg.itp"

#endif

; Include water topology

#include "charmm27.ff/tip3p.itp"


 Everything seems to be ok!
Any clue why is that?
 



The topology must follow a defined order.  Please consult Chapter 5
of the manual for the required hierarchy.  Of course, the latter
case will also not work, because you've introduced ligand position
restraints after the protein [moleculetype], so if invoked, they
will cause a different fatal error.

The Gromacs site also has more on these types of errors, as well as
the list archive, where this error has been posted and solved
hundreds of times.

-Justin

Thank you Justin! But actually the last case I provided actually
works...



Then the position restraints are not being applied to the ligand.  They can't 
be.  Once the protein [moleculetype] is introduced, all [position_restraints] 
directives immediately after are applied to it.  Try invoking the restraints 
separately, i.e. with "define = -DPOSRES -DPOSRES_LIGAND" and you will get a 
fatal error.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Ligand topology in topol.top

[Steven Neumann]

On Tue, Nov 1, 2011 at 5:44 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>
>>
>> On Tue, Nov 1, 2011 at 4:11 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Steven Neumann wrote:
>>
>>Hi Guys,
>> I am using Charmm27 ff for my protein and ligand system. I used
>>SwissParam to generate the topology for my ligand. I included
>>the obtained topology of my ligand as in Justin tutorial:
>> ; Include Position restraint file
>>
>>#ifdef POSRES
>>
>>#include "posre.itp"
>>
>>#endif
>>
>>; Include ligand topology
>>
>>#include "ligand.itp"
>>
>>; Ligand position restraints
>>
>>#ifdef POSRES
>>
>>#include "posre_ligand.itp"
>>
>>#endif
>>
>>; Include water topology
>>
>>#include "charmm27.ff/tip3p.itp"
>>
>> When I wanted to run NVT I obtained:
>> Fatal error:
>>Syntax error - File egcg.itp, line 7
>>Last line read:
>>'[ atomtypes ] '
>>Invalid order for directive atomtypes
>> However when I included my topology as:
>> ; Include forcefield parameters
>>
>>#include "charmm27.ff/forcefield.itp"
>>
>>#include "ligand.itp"
>>
>>[ moleculetype ]
>>
>>; Name nrexc
>>
>>..
>>
>>; Include Position restraint file
>>
>>#ifdef POSRES
>>
>>#include "posre.itp"
>>
>>#endif
>>
>>; Ligand position restraints
>>
>>#ifdef POSRES
>>
>>#include "posre_egcg.itp"
>>
>>#endif
>>
>>; Include water topology
>>
>>#include "charmm27.ff/tip3p.itp"
>>
>>
>> Everything seems to be ok!
>>Any clue why is that?
>>
>>
>>The topology must follow a defined order.  Please consult Chapter 5
>>of the manual for the required hierarchy.  Of course, the latter
>>case will also not work, because you've introduced ligand position
>>restraints after the protein [moleculetype], so if invoked, they
>>will cause a different fatal error.
>>
>>The Gromacs site also has more on these types of errors, as well as
>>the list archive, where this error has been posted and solved
>>hundreds of times.
>>
>>-Justin
>>
>>Thank you Justin! But actually the last case I provided actually
>>works...
>>
>>
> Then the position restraints are not being applied to the ligand.  They
> can't be.  Once the protein [moleculetype] is introduced, all
> [position_restraints] directives immediately after are applied to it.  Try
> invoking the restraints separately, i.e. with "define = -DPOSRES
> -DPOSRES_LIGAND" and you will get a fatal error.
>
>
> -Justin
>


You are as always right :) Thanks!

Steven
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[gmx-users] g_analyze errors

[Alex]

Dear all,

I run a NPT equilibration (1 ns - 1000 steps) and then I drew pressure graph 
using g_energy.
I've tried to run the following command

g_analyze -f pressure.xvg  -av average.xvg -ee errest.xvg

G_ANALYZE PRESSURE***
But I get the following output

Read 1 sets of 5001 points, dt = 0.2

  std. dev.relative deviation of
   standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
  cum. 3   cum. 4
SS1   7.234428e-01   1.087484e+02   1.537935e+00  -0.0210.049


Data set 1 has strange time correlations:
the std. error using single points is larger than that of blocks of 2 points
The error estimate might be inaccurate, check the fit
a fitted parameter is negative
invalid fit:  e.e. 0.627815  a 1.14495  tau1 0.1214  tau2 0.843945
Will fix tau2 at the total time: 1000
Set   1:  err.est. 24.0042  a 0.975634  tau1 1.56619e-05  tau2 1000
**

Then I run g_energy to get Box_X and Box_Y values and I run the following:

g_analyze -f box_x.xvg  -av average.xvg -ee errest.xvg 

Here is the output

G_ANALYZE BOX_X***
Read 1 sets of 5001 points, dt = 0.2

  std. dev.relative deviation of
   standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
  cum. 3   cum. 4
SS1   1.363121e+01   3.707014e-02   5.242510e-04   0.031   -0.354
a fitted parameter is negative
invalid fit:  e.e. -nan  a 0.0250074  tau1 0.501456  tau2 -960816
Will fix tau2 at the total time: 1000
a fitted parameter is negative
invalid fit:  e.e. 0.0665633  a -3.59838  tau1 829.806  tau2 1000
Will use a single exponential fit for set 1
Set   1:  err.est. 0.0969565  a 1  tau1 3421.07  tau2 0
**


How can I fix these errors? Could you give me any suggestion?

Thank in advance

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[gmx-users] Re:Re: PCA on secondary structure of protein.

[vivek modi]

Thanks a lot Tsjerk.
I really appreciate the help.



Regards,
-Vivek.




> Message: 6
> Date: Tue, 1 Nov 2011 17:35:54 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] PCA on secondary structure of protein.
> To: Discussion list for GROMACS users 
> Message-ID:
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Sure!
>
> You'll just be looking at correlations between secondary structure
> elements, disregarding the role that the loops may play. But it's a
> sound approach.
>
> :)
>
> Tsjerk
>
> On Tue, Nov 1, 2011 at 3:44 PM, vivek modi 
> wrote:
> > Hi,
> >
> > I plan to perform PCA on a globular protein which I am studying. The
> > simulation for the same is done for 100ns.
> > I have small doubt. Is it appropriate to perform PCA to study the
> movement
> > in protein on only secondary structure elements (helices in this case).
> > My protein contains long loops which do not play any role. Is it
> appropriate
> > to group only the helices together ignoring the loops and perform PCA ?
> >
> > Any help is appreciated.
> >
> >
> > Regards,
> >
> > -Vivek Modi
> > Graduate Student
> > IITK.
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
> --
>
>
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[gmx-users] re: Phosphate esters

[Ben Ahmady]

Dear GROMACS users/developers

I've recently started a PhD and am currently looking at bilayer 
formation of two-tailed alkyl phosphate esters. I've been using the 
PRODRG server to generate topologies for use in GROMACS, and as per the 
recommendations made in the paper by Lemkul et. al I have consistently 
altered the charges/charge groups according to the charges reported in 
similar molecules for which topologies are well established. However, 
the "similar molecules" to which I'm referring to are phospholipids such 
as DPPC rather than the alkyl phosphate esters in which I'm interested, 
and as such I was concerned that the charges [for the alkyl phosphates] 
I was implementing might not be entirely accurate. I therefore set about 
rather ham-fistedly doing Bader analysis on the individual alkyl 
phosphate molecules I'm studying to try to establish more realistic 
charges to implement in the topology (more accurately: I ran the same 
simulations concurrently with the established molecules like DPPC and 
tried to find a relationship between their Bader charges and topologies 
which I could use to make a realistic estimate of the charges on the 
alkyl phosphate molecules).


I really have two questions and hoped that I might take the opportunity 
to ask experienced users/scientists: the first is whether I'm wrong and 
that in your opinion(s) it is in fact sensible to simply use the charges 
from, say, DPPC in my alkyl phosphate molecules, and the second question 
is - regardless of the answer to the first question - whether what I'm 
doing is in your opinion(s) sensible. I hope these aren't inappropriate 
questions.



Many thanks

--
Ben Ahmady
EngD candidate
M3S Doctoral Training Centre
University College London

Please try to avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

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[gmx-users] grompp: "invalid bond type" error

[Olivia Waring]

Dear Gromacs users,

First of all, many thanks to Justin for his assistance with my previous
question.

I have defined a new residue type in the oplsaa force field, changing the
aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try
to preprocess, I get the following output:

WARNING 1 [file ffbonded.itp, line 58]:
  Overriding Bond parameters.

  old: 0.1229 476976 0.1229 476976
  new: C O  10.13270   179075.2


WARNING 2 [file ffbonded.itp, line 64]:
  Overriding Bond parameters.

  old: 0.1522 265266 0.1522 265266
  new: CCT  10.14950   265265.6


WARNING 3 [file ffbonded.itp, line 67]:
  Overriding Bond parameters.

  old: 0.149 334720 0.149 334720
  new: CAC  10.14240   392459.2


WARNING 4 [file ffbonded.itp, line 73]:
  Overriding Bond parameters.

  old: 0.1419 374050 0.1419 374050
  new: CCB  10.14240   392459.2


---
Program grompp, VERSION 4.5.4
Source code file: topdirs.c, line: 76

Fatal error:
Invalid bond type 0
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


The error is rather cryptic, and I'm having trouble tracking it down... I
even went to the source code (topdirs.c), but I'm still not sure where
exactly this "invalid bond type" is being defined.

Thank you so much for your help,
Olivia


-- 
Olivia Waring (王维娅)
Princeton University '12
AB Chemistry
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Re: [gmx-users] grompp: "invalid bond type" error

[Justin A. Lemkul]

Olivia Waring wrote:

Dear Gromacs users,

First of all, many thanks to Justin for his assistance with my previous 
question.


I have defined a new residue type in the oplsaa force field, changing 
the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when 
I try to preprocess, I get the following output: 


WARNING 1 [file ffbonded.itp, line 58]:
  Overriding Bond parameters.

  old: 0.1229 476976 0.1229 476976
  new: C O  10.13270   179075.2


WARNING 2 [file ffbonded.itp, line 64]:
  Overriding Bond parameters.

  old: 0.1522 265266 0.1522 265266
  new: CCT  10.14950   265265.6


WARNING 3 [file ffbonded.itp, line 67]:
  Overriding Bond parameters.

  old: 0.149 334720 0.149 334720
  new: CAC  10.14240   392459.2


WARNING 4 [file ffbonded.itp, line 73]:
  Overriding Bond parameters.

  old: 0.1419 374050 0.1419 374050
  new: CCB  10.14240   392459.2



These four warnings suggest you're using values for bonded parameters that 
conflict with those present in the force field.  If you have reason to do this, 
then there's no problem, per se.  But be aware that you're using parameters the 
force field does not expect.




---
Program grompp, VERSION 4.5.4
Source code file: topdirs.c, line: 76

Fatal error:
Invalid bond type 0
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


The error is rather cryptic, and I'm having trouble tracking it down... 
I even went to the source code (topdirs.c), but I'm still not sure where 
exactly this "invalid bond type" is being defined. 



This error suggests a more fundamental problem in your topology, but without 
seeing the topology, there's little more that can be said.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] grompp: "invalid bond type" error

[Olivia Waring]

Thank you so much for your quick reply!

Below please find my topology file:


; Include forcefield parameters
#include "hautklein.ff/forcefield.itp"

[ moleculetype ]
; Namenrexcl
Protein_chain_1 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
; residue   0 ALK rtp ALK  q  0.0
 1CH3  0ALKCH3  1  0 15.035   ;
qtot 0
 2CH2  0ALK   CH2A  2  0 14.027   ;
qtot 0
 3CH2  0ALK   CH2B  3  0 14.027   ;
qtot 0
 4CH2  0ALK   CH2C  4  0 14.027   ;
qtot 0
 5CH2  0ALK   CH2D  5  0 14.027   ;
qtot 0
 6CH2  0ALK   CH2E  6  0 14.027   ;
qtot 0
 7CH2  0ALK   CH2F  7  0 14.027   ;
qtot 0
 8CH2  0ALK   CH2G  8  0 14.027   ;
qtot 0
 9CH2  0ALK   CH2H  9  0 14.027   ;
qtot 0
10CH2  0ALK   CH2I 10  0 14.027   ;
qtot 0
11CH2  0ALK   CH2J 11  0 14.027   ;
qtot 0
12CH2  0ALK   CH2K 12  0 14.027   ;
qtot 0
13  S  0ALK  S 13  0  32.06   ;
qtot 0

[ bonds ]
;  aiaj functc0c1c2c3
1 2 1
2 3 1
3 4 1
4 5 1
5 6 1
6 7 1
7 8 1
8 9 1
910 1
   1011 1
   1112 1
   1213 1

[ pairs ]
;  aiaj functc0c1c2c3
1 4 1
2 5 1
3 6 1
4 7 1
5 8 1
6 9 1
710 1
811 1
912 1
   1013 1

[ angles ]
;  aiajak functc0c1c2
 c3
1 2 3 1
2 3 4 1
3 4 5 1
4 5 6 1
5 6 7 1
6 7 8 1
7 8 9 1
8 910 1
91011 1
   101112 1
   111213 1

[ dihedrals ]
;  aiajakal functc0c1c2
   c3c4c5
1 2 3 4 3
2 3 4 5 3
3 4 5 6 3
4 5 6 7 3
5 6 7 8 3
6 7 8 9 3
7 8 910 3
8 91011 3
9101112 3
   10111213 3

[ constraints ]
;   i j funct   b0
1 2 1   0.0153
2 3 1   0.0153
3 4 1   0.0153
4 5 1   0.0153
5 6 1   0.0153
6 7 1   0.0153
7 8 1   0.0153
8 9 1   0.0153
9 101   0.0153
10111   0.0153
11121   0.0153
12131   0.0182

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_chain_1 1

Does this help?

Thanks so much again,
Olivia

On Tue, Nov 1, 2011 at 5:49 PM, Justin A. Lemkul  wrote:

>
>
> Olivia Waring wrote:
>
>> Dear Gromacs users,
>>
>> First of all, many thanks to Justin for his assistance with my previous
>> question.
>>
>> I have defined a new residue type in the oplsaa force field, changing the
>> aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try
>> to preprocess, I get the following output:
>> WARNING 1 [file ffbonded.itp, line 58]:
>>  Overriding Bond parameters.
>>
>>  old: 0.1229 476976 0.1229 476976
>>  new: C O  10.13270   179075.2
>>
>>
>> WARNING 2 [file ffbonded.itp, line 64]:
>>  Overriding Bond parameters.
>>
>>  old: 0.1522 265266 0.1522 265266
>>  new: CCT  10.14950   265265.6
>>
>>
>> WARNING 3 [file ffbonded.itp, line 67]:
>>  Overriding Bond parameters.
>>
>>  old: 0.149 334720 0.149 334720
>>  new: CAC  10.14240   392459.2
>>
>>
>> WARNING 4 [file ffbonded.itp, line 73]:
>>  Overriding Bond parameters.
>>
>>  old: 0.1419 374050 0.1419 374050
>>  new: CCB  10.14240   392459.2
>>
>>
> These four warnings suggest you're using values for bonded parameters that
> conflict with those present in the force field.  If you have reason to do
> this, then there's no problem, per se.  But be aware that you're using
> parameters the force field does not expect.
>
>
>
>> --**-
>> Program grompp, VERSION 4.5.4
>> Source code file: topdirs.c, line: 76
>>
>> Fatal error:
>> Invalid bond type 0
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/*

Re: [gmx-users] grompp: "invalid bond type" error

[Justin A. Lemkul]

Olivia Waring wrote:

Thank you so much for your quick reply!

Below please find my topology file: 



; Include forcefield parameters
#include "hautklein.ff/forcefield.itp"



The problems you are experiencing are probably coming from this file, or perhaps 
somewhere else in your custom force field.  The error suggests that your 
[defaults] directive is improperly constructed.


-Justin


[ moleculetype ]
; Namenrexcl
Protein_chain_1 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass 
 typeBchargeB  massB

; residue   0 ALK rtp ALK  q  0.0
 1CH3  0ALKCH3  1  0 15.035   ; 
qtot 0
 2CH2  0ALK   CH2A  2  0 14.027   ; 
qtot 0
 3CH2  0ALK   CH2B  3  0 14.027   ; 
qtot 0
 4CH2  0ALK   CH2C  4  0 14.027   ; 
qtot 0
 5CH2  0ALK   CH2D  5  0 14.027   ; 
qtot 0
 6CH2  0ALK   CH2E  6  0 14.027   ; 
qtot 0
 7CH2  0ALK   CH2F  7  0 14.027   ; 
qtot 0
 8CH2  0ALK   CH2G  8  0 14.027   ; 
qtot 0
 9CH2  0ALK   CH2H  9  0 14.027   ; 
qtot 0
10CH2  0ALK   CH2I 10  0 14.027   ; 
qtot 0
11CH2  0ALK   CH2J 11  0 14.027   ; 
qtot 0
12CH2  0ALK   CH2K 12  0 14.027   ; 
qtot 0
13  S  0ALK  S 13  0  32.06   ; 
qtot 0


[ bonds ]
;  aiaj functc0c1c2c3
1 2 1
2 3 1
3 4 1
4 5 1
5 6 1
6 7 1
7 8 1
8 9 1
910 1
   1011 1
   1112 1
   1213 1

[ pairs ]
;  aiaj functc0c1c2c3
1 4 1
2 5 1
3 6 1
4 7 1
5 8 1
6 9 1
710 1
811 1
912 1
   1013 1

[ angles ]
;  aiajak functc0c1c2   
 c3

1 2 3 1
2 3 4 1
3 4 5 1
4 5 6 1
5 6 7 1
6 7 8 1
7 8 9 1
8 910 1
91011 1
   101112 1
   111213 1

[ dihedrals ]
;  aiajakal functc0c1c2 
   c3c4c5

1 2 3 4 3
2 3 4 5 3
3 4 5 6 3
4 5 6 7 3
5 6 7 8 3
6 7 8 9 3
7 8 910 3
8 91011 3
9101112 3
   10111213 3

[ constraints ]
;   i j funct   b0
1 2 1   0.0153
2 3 1   0.0153
3 4 1   0.0153
4 5 1   0.0153
5 6 1   0.0153
6 7 1   0.0153
7 8 1   0.0153
8 9 1   0.0153
9 101   0.0153
10111   0.0153
11121   0.0153
12131   0.0182

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
Protein_chain_1 1
  
Does this help?


Thanks so much again,
Olivia   

On Tue, Nov 1, 2011 at 5:49 PM, Justin A. Lemkul > wrote:




Olivia Waring wrote:

Dear Gromacs users,

First of all, many thanks to Justin for his assistance with my
previous question.

I have defined a new residue type in the oplsaa force field,
changing the aminoacids.rtp file accordingly. pdb2gmx worked
just fine; but when I try to preprocess, I get the following
output:
WARNING 1 [file ffbonded.itp, line 58]:
 Overriding Bond parameters.

 old: 0.1229 476976 0.1229 476976
 new: C O  10.13270   179075.2


WARNING 2 [file ffbonded.itp, line 64]:
 Overriding Bond parameters.

 old: 0.1522 265266 0.1522 265266
 new: CCT  10.14950   265265.6


WARNING 3 [file ffbonded.itp, line 67]:
 Overriding Bond parameters.

 old: 0.149 334720 0.149 334720
 new: CAC  10.14240   392459.2


WARNING 4 [file ffbonded.itp, line 73]:
 Overriding Bond parameters.

 old: 0.1419 374050 0.1419 374050
 new: CCB  10.14240   392459.2


These four warnings suggest you're using values for bonded
parameters that conflict with those present in the force fie

Re: [gmx-users] grompp: "invalid bond type" error

[Mark Abraham]

On 2/11/2011 8:32 AM, Olivia Waring wrote:

Dear Gromacs users,

First of all, many thanks to Justin for his assistance with my 
previous question.


I have defined a new residue type in the oplsaa force field, changing 
the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but 
when I try to preprocess, I get the following output:


WARNING 1 [file ffbonded.itp, line 58]:


You'll need to inspect at and before this line in this file to diagnose.

Mark


  Overriding Bond parameters.

  old: 0.1229 476976 0.1229 476976
  new: C O  10.13270   179075.2


WARNING 2 [file ffbonded.itp, line 64]:
  Overriding Bond parameters.

  old: 0.1522 265266 0.1522 265266
  new: CCT  10.14950   265265.6


WARNING 3 [file ffbonded.itp, line 67]:
  Overriding Bond parameters.

  old: 0.149 334720 0.149 334720
  new: CAC  10.14240   392459.2


WARNING 4 [file ffbonded.itp, line 73]:
  Overriding Bond parameters.

  old: 0.1419 374050 0.1419 374050
  new: CCB  10.14240   392459.2


---
Program grompp, VERSION 4.5.4
Source code file: topdirs.c, line: 76

Fatal error:
Invalid bond type 0
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors


The error is rather cryptic, and I'm having trouble tracking it 
down... I even went to the source code (topdirs.c), but I'm still not 
sure where exactly this "invalid bond type" is being defined.


Thank you so much for your help,
Olivia


--
Olivia Waring (???)
Princeton University '12
AB Chemistry





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[gmx-users] CG representation for Organic molecules

[Venkat Reddy]

Dear All,
I would like to run CG Dynamics for my system, which includes two organic
molecules (GTP,GDP) and Mg2+ ion. I would like to add K+ and CL- as counter
balancing ions. I have referred the MARTINI tutorial web page, but there is
nothing about HETATM inclusion. Please help me in this regard.

Thanking you


With Best Wishes
Venkat Reddy Chirasani
IIT Madras
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