Re: [gmx-users] g_rotacf

[Xavier Periole]

On Wed, 3 Sep 2008 23:40:14 -0400
 "rams rams" <[EMAIL PROTECTED]> wrote:

Hi,

I am so surprised for not finding any one who have better experience with
g_rotacf. I have been playing around with it and the time correlation value
I got by g_rotacf is so small in comparison to the time correlation value I
calcualted using the hydrodynamic radius of the protein. The value is nearly
10 times less. Can some one give me a better idea about g_rotacf.

Many people have certainly used g_rotacf to get ACFs of different observables.

Anyways the way you describe your system, command line and your problem does
does not help anyone to help you. Read your message above and think about what
you would answer! You've played around with g_rotacf therefore you know it
is not straightforward to give you the magic command.

XAvier.


Ram.


-
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-
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[gmx-users] g_rotacf

[rams rams]

Hi,

I am so surprised for not finding any one who have better experience with
g_rotacf. I have been playing around with it and the time correlation value
I got by g_rotacf is so small in comparison to the time correlation value I
calcualted using the hydrodynamic radius of the protein. The value is nearly
10 times less. Can some one give me a better idea about g_rotacf.

Ram.
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Re: [gmx-users] Re: Bonds break while Minimising using distance restraints

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:

My protein has 5 chains. 1703 & 1712 are the numbers from chainC.itp 
file. This includes the distance restraints -


#ifdef DDISRES
[ distance_restraints ]
;ai   aj type index type' low   up1  up2  fac
1703 1712 10 11.15  1.20 1.25 1.0
#endif

6151 & 6160 atoms are the numbers from .gro file reported by the .job 
file. 6151 is N of residue 584 and 1703 is CA of the same redsidue. 
Residue 584 & 585 are placed have 14 residues missing between them. 6160 
is N of residue 585 &  1712 is the corresponding CA.


So you have an incomplete protein backbone, with some odd numbering.  What 
command did you give pdb2gmx to generate this topology?  Did you use the 
-missing flag?  If so, the topology may be badly broken and unexpected bonds 
defined.  Look closely at your [ bonds ] section in "chain_C.itp" in case you 
have some bonds that you are not expecting!


Do you have complete residues for each of those that contain atoms 6151, 6160, 
1703 and 1712?  The non-sequential numbering (with 4000-atom separation!) does 
not indicate that these atoms should be in the same residues.


Is your structure one that is available in the PDB?  Perhaps it would be much 
easier to diagnose this if I could see the structure.  I'd be willing to have a 
look at your structure file, if you'd like to send it to me privately.  I'm 
somewhat intrigued as to what the problem is :)


I would be willing to bet that there is something within that chain topology 
that is causing mdrun to find a 1-4 interaction between atoms 6151 and 6160.


-Justin




Thanks & regards,
Latha.


- Original Message -
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Date: Wednesday, September 3, 2008 5:36 pm
Subject: Re: Bonds break while Minimising using distance restraints
To: [EMAIL PROTECTED], Gromacs Users' List 

 >
 >
 > [EMAIL PROTECTED] wrote:
 > > Hi Justin,
 > >
 > >   Thanks for your prompt
 > suggestions.  I hope I didn't cause any
 > > sort of inconvenience by E-mailing you directly.
 > >
 >
 > I say this constantly - it is always better to keep the
 > discussion on the list
 > so that, if I don't have the complete right answer (which
 > happens often!)
 > someone else can weigh in and help out.  It is also helpful
 > to complete
 > discussions in the archives.  There's nothing more
 > frustrating than finding your
 > exact problem in the archives, only to find out that the thread
 > dies off without
 > a solution :)
 >
 > >  >I thought you were applying a 12-nm distance restrain
 > to atoms in the
 > > 7000's, so
 > >  >I'm confused as to why atoms615 1 and 6160 should be 12
 > nm apart
 > > (assuming, of
 > >  >course, that you meant to say nm instead of A :)
 > >
 > >  I am sorry for the confusion.
 > The atoms are separated by 12 A (1.2
 > > nm). The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms
 > are also
 > > from the same residues). These are the residues that looks as
 > if they
 > > are no bonds between them. ( residues alone, peptide bond
 > alone and the
 > > rest of the protein).
 >
 > How is it that atoms that are 900 indices apart are in the same
 > residues.  I
 > don't understand.  Do you mean that all four of these atoms
 > are in the same
 > residue?  Then they definitely aren't amino acids! 
 > Are these two separate

 > residues bridged by a distance restraint, that you are
 > considering one residue?
 >   Is there some bond defined in the topology between *any*
 > of these atoms?
 >
 > >
 > > While doing grompp I get the following "removed 1 distance
 > restraints".
 > > Does this mean, the distance restraint isn't imposed at all?
 > >
 >
 > That would be a pretty clear indication to me that distance
 > restraints are not
 > being applied.
 >
 > >  I corrected the distance restraints I used as
 > >
 > > #ifdef DDISRES
 > > [distance_restraints]
 > > ;ai   aj type index type' low up1  
 > up2  fac
 > > 1703 1712 10
 > 11.15  1.20 1.25 1.0

 > > #endif
 > >
 >
 > Then, are you correctly applying "define = -DDDISRES" in your
 > .mdp as I
 > suggested previously?
 >
 > http://www.gromacs.org/pipermail/gmx-users/2008-September/036136.html
 >
 > -Justin
 >
 > > I endup with the same error. Is there any possible way to get
 > over this
 > > problem?
 > >
 > > I appreciate your help in this regard.
 > >
 > > wamr regards,
 > > Latha.
 > >
 > >
 > >  >  There is no chance of
 > steric clashes between 6151 & 6160. They are
 > >  > seperated by 12 A. ("Warning: 1-4 interaction between
 > 6151 and 6160 at
 > >  > distance 1.387 which is larger than the 1-4 table size
 > 1.000 nm. These
 > >  > are ignored for the rest of the simulation. This
 > usually means your
 > >  > system is exploding") I cannot build the missing
 > residues without
 > >  > knowing the secondary structure. I am already running
 > one simulation
 > >  > with built residues. But, my ultimate goal is to run
 > dynamics with
 > >  > distance restraints.
 > >
 > > Are you sure you are iden

[gmx-users] Re: Bonds break while Minimising using distance restraints

[plmallip]

Hi,


The atoms are separated by 12 A (1.2
> nm). The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are also
> from the same residues). These are the residues that looks as if they
> are no bonds between them. ( residues alone, peptide bond alone and the
> rest of the protein).

How is it that atoms that are 900 indices apart are in the same residues.  I
don't understand.  Do you mean that all four of these atoms are in the same
residue?  Then they definitely aren't amino acids!  Are these two separate
residues bridged by a distance restraint, that you are considering one residue?
  Is there some bond defined in the topology between *any* of these atoms?

My protein has 5 chains. 1703 & 1712 are the numbers from chainC.itp file. This 
includes the distance restraints -

#ifdef DDISRES
[ distance_restraints ]
;ai   aj type index type' low   up1  up2  fac
1703 1712 1    0 1    1.15  1.20 1.25 1.0
#endif

6151 & 6160 atoms are the numbers from .gro file reported by the .job file. 
6151 is N of residue 584 and 1703 is CA of the same redsidue. Residue 584 & 585 
are placed have 14 residues missing between them. 6160 is N of residue 585 &  
1712 is the corresponding CA.

>Then, are you correctly applying "define = -DDDISRES" in your .mdp as I
>suggested previously?

I did correctly use the -DDDISRES, as suggested by you, which is as follows:

title   =  ${MOL}
cpp =  /lib/cpp
define  = -DDDISRES


Thanks & regards,
Latha.


- Original Message -
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Date: Wednesday, September 3, 2008 5:36 pm
Subject: Re: Bonds break while Minimising using distance restraints
To: [EMAIL PROTECTED], Gromacs Users' List 

> 
> 
> [EMAIL PROTECTED] wrote:
> > Hi Justin,
> > 
> >   Thanks for your prompt 
> suggestions.  I hope I didn't cause any 
> > sort of inconvenience by E-mailing you directly. 
> > 
> 
> I say this constantly - it is always better to keep the 
> discussion on the list 
> so that, if I don't have the complete right answer (which 
> happens often!) 
> someone else can weigh in and help out.  It is also helpful 
> to complete 
> discussions in the archives.  There's nothing more 
> frustrating than finding your 
> exact problem in the archives, only to find out that the thread 
> dies off without 
> a solution :)
> 
> >  >I thought you were applying a 12-nm distance restrain 
> to atoms in the 
> > 7000's, so
> >  >I'm confused as to why atoms615 1 and 6160 should be 12 
> nm apart 
> > (assuming, of
> >  >course, that you meant to say nm instead of A :)
> > 
> >  I am sorry for the confusion. 
> The atoms are separated by 12 A (1.2 
> > nm). The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms 
> are also 
> > from the same residues). These are the residues that looks as 
> if they 
> > are no bonds between them. ( residues alone, peptide bond 
> alone and the 
> > rest of the protein).
> 
> How is it that atoms that are 900 indices apart are in the same 
> residues.  I 
> don't understand.  Do you mean that all four of these atoms 
> are in the same 
> residue?  Then they definitely aren't amino acids!  
> Are these two separate 
> residues bridged by a distance restraint, that you are 
> considering one residue? 
>   Is there some bond defined in the topology between *any* 
> of these atoms?
> 
> > 
> > While doing grompp I get the following "removed 1 distance 
> restraints". 
> > Does this mean, the distance restraint isn't imposed at all?
> > 
> 
> That would be a pretty clear indication to me that distance 
> restraints are not 
> being applied.
> 
> >  I corrected the distance restraints I used as
> > 
> > #ifdef DDISRES
> > [distance_restraints]
> > ;ai   aj type index type' low up1   
> up2  fac
> > 1703 1712 1    0 
> 1    1.15  1.20 1.25 1.0
> > #endif
> > 
> 
> Then, are you correctly applying "define = -DDDISRES" in your 
> .mdp as I 
> suggested previously?
> 
> http://www.gromacs.org/pipermail/gmx-users/2008-September/036136.html
> 
> -Justin
> 
> > I endup with the same error. Is there any possible way to get 
> over this 
> > problem?
> > 
> > I appreciate your help in this regard.
> > 
> > wamr regards,
> > Latha.
> > 
> > 
> >  >  There is no chance of 
> steric clashes between 6151 & 6160. They are
> >  > seperated by 12 A. ("Warning: 1-4 interaction between 
> 6151 and 6160 at
> >  > distance 1.387 which is larger than the 1-4 table size 
> 1.000 nm. These
> >  > are ignored for the rest of the simulation. This 
> usually means your
> >  > system is exploding") I cannot build the missing 
> residues without
> >  > knowing the secondary structure. I am already running 
> one simulation
> >  > with built residues. But, my ultimate goal is to run 
> dynamics with
> >  > distance restraints.
> > 
> > Are you sure you are identifying the correct atoms?  A 1-
> 4 interaction 
> > involves
> > atoms that are very close together (in fact, three bonds 
> away).  Are you 
> > saying

Re: [gmx-users] Re: Re: Bonds break while Minimising using distance restraints

[plmallip]

- Original Message -
From: Ryogo Sugitani <[EMAIL PROTECTED]>
Date: Wednesday, September 3, 2008 5:46 pm
Subject: Re: [gmx-users] Re: Re: Bonds break while Minimising using distance 
restraints
To: [EMAIL PROTECTED]

> Latha,
> 
> I'm not sure why there is 1-4 interaction between 6151 and 6160
> by just making distance restraint between 1703 and 1712
> (because they shouldn't make a physical bond...)
> 
> but maybe adding space before and after distace_restraints 
> (between brackets) might help?
> Also, check the trajectory on VMD. 
> The warning is given, but md (or minimization) itself might be 
> running fine...
> 
> Other than this, I probably won't be able to help you any further.
> 
> Also, please post it back to gmx-ml for me...
> (just reply to this message and change the address to gmx's list)
> 
> Thanks,
> 
> Ryogo
> 
> 
> 
> On Wed, 03 Sep 2008 16:43:45 -0500, [EMAIL PROTECTED] wrote:
> > Hi Ryogo,
> > 
> >  Thanks 
> for your suggestion. You are right. But, I did do the 
> > energy minimization assuming the units are in nm But, I am 
> still 
> > facing the same problem of the residues to which I imposed 
> distance 
> > restraint breaking into fragments. I get this warning -  
> 1-4 
> > interaction between 6151 and 6160 at distance 1.387 which is 
> larger 
> > than the 1-4 table size 1.000 > nm. These are ignored for the 
> rest of 
> > the simulation. This 
> > usually means your system is exploding. 
> > 
> > Do you have any other suggestions?
> > 
> > Thanks & regards,
> > Latha.
> > 
> > - Original Message -
> > From: Ryogo Sugitani <[EMAIL PROTECTED]>
> > Date: Wednesday, September 3, 2008 2:58 pm
> > Subject: Re: [gmx-users] Re: Re: Bonds break while Minimising 
> using 
> > distance restraints
> > To: [EMAIL PROTECTED]
> > 
> >> Hi Latha,
> >> 
> >> Since I cannot post it to the gmx ML directly for some 
> reason, 
> >> I'll just give this  e-mail to you.
> >> 
> >> I believe the unit for the distance used in 
> distance_restraints 
> >> is nm.
> >> So, you should change it to something like 1.15 1.20 1.20 for 
> >> your setting.
> >> Currently you have 115A, 120A, 120A...
> >> 
> >> Hope that helps,
> >> 
> >> Best,
> >> 
> >> Ryogo
> >> 
> >> 
> >> On Wed, 03 Sep 2008 13:27:06 -0500, [EMAIL PROTECTED] wrote:
> >>> Hi,
> >>> 
> >>>   There is no chance of 
> steric 
> >> clashes between 6151 & 6160. They 
> >>> are seperated by 12 A. ("Warning: 1-4 interaction between 
> 6151 
> >> and 
> >>> 6160 at distance 1.387 which is larger than the 1-4 table 
> size 
> >> 1.000 
> >>> nm. These are ignored for the rest of the simulation. This 
> >> usually 
> >>> means your system is exploding") I cannot build the missing 
> >> residues 
> >>> without knowing the secondary structure. I am already 
> running 
> >> one 
> >>> simulation with built residues. But, my ultimate goal is to 
> >> run 
> >>> dynamics with distance restraints.
> >>>   
> >>> My sytem is 
> an 
> >> pentamer. Here is the toplogy file
> >>> 
> >>> ; Include forcefield parameters
> >>> #include "ffG43a1.itp"
> >>> 
> >>> ; Include chain topologies
> >>> #include "chnrc_A.itp"
> >>> #include "chnrc_B.itp"
> >>> #include "chnrc_C.itp"
> >>> #include "chnrc_D.itp"
> >>> #include "chnrc_E.itp"
> >>> 
> >>> ; Include water topology
> >>> #include "spce.itp"
> >>> 
> >>> #ifdef POSRES_WATER
> >>> ; Position restraint for each water oxygen
> >>> [ position_restraints ]
> >>> ;  i funct   
> >> fcx    
> fcy    fcz
> >>> 1    
> >> 1   
> 1000   1000   1000
> >>> #endif
> >>> 
> >>> ; Include generic topology for ions
> >>> #include "ions.itp"
> >>> 
> >>> [ system ]
> >>> ; Name
> >>> Protein in water
> >>> 
> >>> [ molecules ]
> >>> ; Compound    #mols
> >>> 
> >> 
> Protein_A   1
> >>> 
> >> 
> Protein_B   1
> >>> 
> >> 
> Protein_C   1
> >>> 
> >> 
> Protein_D   1
> >>> 
> >> 
> Protein_E   1
> >>> 
> >> 
> SOL  55419
> >>> 
> >> 
> NA+  54
> >>> 
> >>> 
> >>> Thanks & regards,
> >>> Latha.
> >>> 
> > [EMAIL PROTECTED] wrote:
> > 
> > Hi Justin, thanks for your response. You are right. I get 
> >> the 
>  following 
> > message in the .job file
> > 
> > "Warning: 1-4 interaction between 6151 and 6160 at 
> distance 
>  1.387 which 
> > is larger than the 1-4 table size 1.000 nm
> > These are ignored for the rest of the simulation
> > This usually means your system is exploding"
> > 
> > The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms 
> >> are 
>  also from 
> > the same residues). The distance between them is 12 A 
> (there 
>  are 14 
> > missing residues in between). My aim is to use distance 
>  restraints, 
> > without building missing residues in between. Is there any 
> >> way 
>  I can 
> > overcome this warning why minimizing the system?
>  
>  It's very hard to say, because none

[gmx-users] Re: Bonds break while Minimising using distance restraints

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:

Hi Justin,

  Thanks for your prompt suggestions.  I hope I didn't cause any 
sort of inconvenience by E-mailing you directly. 



I say this constantly - it is always better to keep the discussion on the list 
so that, if I don't have the complete right answer (which happens often!) 
someone else can weigh in and help out.  It is also helpful to complete 
discussions in the archives.  There's nothing more frustrating than finding your 
exact problem in the archives, only to find out that the thread dies off without 
a solution :)


 >I thought you were applying a 12-nm distance restrain to atoms in the 
7000's, so
 >I'm confused as to why atoms615 1 and 6160 should be 12 nm apart 
(assuming, of

 >course, that you meant to say nm instead of A :)

 I am sorry for the confusion. The atoms are separated by 12 A (1.2 
nm). The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are also 
from the same residues). These are the residues that looks as if they 
are no bonds between them. ( residues alone, peptide bond alone and the 
rest of the protein).


How is it that atoms that are 900 indices apart are in the same residues.  I 
don't understand.  Do you mean that all four of these atoms are in the same 
residue?  Then they definitely aren't amino acids!  Are these two separate 
residues bridged by a distance restraint, that you are considering one residue? 
 Is there some bond defined in the topology between *any* of these atoms?




While doing grompp I get the following "removed 1 distance restraints". 
Does this mean, the distance restraint isn't imposed at all?




That would be a pretty clear indication to me that distance restraints are not 
being applied.



 I corrected the distance restraints I used as

#ifdef DDISRES
[distance_restraints]
;ai   aj type index type' low up1   up2  fac
1703 1712 10 11.15  1.20 1.25 1.0
#endif



Then, are you correctly applying "define = -DDDISRES" in your .mdp as I 
suggested previously?


http://www.gromacs.org/pipermail/gmx-users/2008-September/036136.html

-Justin

I endup with the same error. Is there any possible way to get over this 
problem?


I appreciate your help in this regard.

wamr regards,
Latha.


 >  There is no chance of steric clashes between 6151 & 6160. They are
 > seperated by 12 A. ("Warning: 1-4 interaction between 6151 and 6160 at
 > distance 1.387 which is larger than the 1-4 table size 1.000 nm. These
 > are ignored for the rest of the simulation. This usually means your
 > system is exploding") I cannot build the missing residues without
 > knowing the secondary structure. I am already running one simulation
 > with built residues. But, my ultimate goal is to run dynamics with
 > distance restraints.

Are you sure you are identifying the correct atoms?  A 1-4 interaction 
involves
atoms that are very close together (in fact, three bonds away).  Are you 
saying
that they are separated by 12 A (1.2 nm) or by 12 nm?  If they are 
starting 12 A

(1.2 nm) away, then the error message still makes sense.  If they are 12 nm
away, then I suspect that some sort of bond or restraint is being applied
improperly.



I thought you were applying a 12-nm distance restrain to atoms in the 
7000's, so
I'm confused as to why atoms615 1 and 6160 should be 12 nm apart 
(assuming, of

course, that you meant to say nm instead of A :)

-Justin

 >
 >My sytem is an pentamer. Here is the toplogy file
 >
 > ; Include forcefield parameters
 > #include "ffG43a1.itp"
 >
 > ; Include chain topologies
 > #include "chnrc_A.itp"
 > #include "chnrc_B.itp"
 > #include "chnrc_C.itp"
 > #include "chnrc_D.itp"
 > #include "chnrc_E.itp"
 >
 > ; Include water topology
 > #include "spce.itp"
 >
 > #ifdef POSRES_WATER
 > ; Position restraint for each water oxygen
 > [ position_restraints ]
 > ;  i funct   fcxfcyfcz
 >11   1000   1000   1000
 > #endif
 >
 > ; Include generic topology for ions
 > #include "ions.itp"
 >
 > [ system ]
 > ; Name
 > Protein in water
 >
 > [ molecules ]
 > ; Compound#mols
 > Protein_A   1
 > Protein_B   1
 > Protein_C   1
 > Protein_D   1
 > Protein_E   1
 > SOL  55419
 > NA+  54
 >
 >
 > Thanks & regards,
 > Latha.
 >
 >  > > [EMAIL PROTECTED] wrote:
 >  > >
 >  > > Hi Justin, thanks for your response. You are right. I get the
 >  > following
 >  > > message in the .job file
 >  > >
 >  > > "Warning: 1-4 interaction between 6151 and 6160 at distance
 >  > 1.387 which
 >  > > is larger than the 1-4 table size 1.000 nm
 >  > > These are ignored for the rest of the simulation
 >  > > This usually means your system is exploding"
 >  > >
 >  > > The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are
 >  > also from
 >  > > the same residues). The distance between them is 12 A (there
 >  > are 14
 >  > > missing residues in between). My aim is to use distance
 >  > restr

Re: [gmx-users] Re: Re: Bonds break while Minimising using distance restraints

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:

Hi,

 There is no chance of steric clashes between 6151 & 6160. They are 
seperated by 12 A. ("Warning: 1-4 interaction between 6151 and 6160 at 
distance 1.387 which is larger than the 1-4 table size 1.000 nm. These 
are ignored for the rest of the simulation. This usually means your 
system is exploding") I cannot build the missing residues without 
knowing the secondary structure. I am already running one simulation 
with built residues. But, my ultimate goal is to run dynamics with 
distance restraints.


Are you sure you are identifying the correct atoms?  A 1-4 interaction involves 
atoms that are very close together (in fact, three bonds away).  Are you saying 
that they are separated by 12 A (1.2 nm) or by 12 nm?  If they are starting 12 A 
(1.2 nm) away, then the error message still makes sense.  If they are 12 nm 
away, then I suspect that some sort of bond or restraint is being applied 
improperly.


I thought you were applying a 12-nm distance restrain to atoms in the 7000's, so 
I'm confused as to why atoms 6151 and 6160 should be 12 nm apart (assuming, of 
course, that you meant to say nm instead of A :)


-Justin

 
   My sytem is an pentamer. Here is the toplogy file


; Include forcefield parameters
#include "ffG43a1.itp"

; Include chain topologies
#include "chnrc_A.itp"
#include "chnrc_B.itp"
#include "chnrc_C.itp"
#include "chnrc_D.itp"
#include "chnrc_E.itp"

; Include water topology
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_A   1
Protein_B   1
Protein_C   1
Protein_D   1
Protein_E   1
SOL  55419
NA+  54


Thanks & regards,
Latha.

 > > [EMAIL PROTECTED] wrote:
 > >
 > > Hi Justin, thanks for your response. You are right. I get the
 > following
 > > message in the .job file
 > >
 > > "Warning: 1-4 interaction between 6151 and 6160 at distance
 > 1.387 which
 > > is larger than the 1-4 table size 1.000 nm
 > > These are ignored for the rest of the simulation
 > > This usually means your system is exploding"
 > >
 > > The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are
 > also from
 > > the same residues). The distance between them is 12 A (there
 > are 14
 > > missing residues in between). My aim is to use distance
 > restraints,
 > > without building missing residues in between. Is there any way
 > I can
 > > overcome this warning why minimizing the system?
 >
 > It's very hard to say, because none of us knows what's in your
 > system, topology,
 > or how you built things :)
 >
 > You have some type of nasty steric clash that's driving atoms
 > 6151 and 6160
 > apart.  Visualize the trajectory (.trr) to see if you can
 > identify where things
 > start to break down.  I don't know if the distance
 > restraint has anything to do
 > with the problem or not.
 >
 > Is there a problem with building missing residues?  That
 > might make life quite a
 > bit easier in the long run.
 >
 > -Justin
 >
 > >
 > > Thanks & regards,
 > > Latha.
 > >
 > >
 > >  > Dear colleagues,
 > >  >
 > >  > I need to use simple distance restraints of 12.5 A
 > between two CA atoms
 > >  > of two residues. I am using the following lines in the
 > .itp file
 > >  >
 > >  > #ifdef DDISRES
 > >  > [distance_restraints]
 > >  > ;ai   aj type index type' low  
 > up1  up2  fac
 > >  > 1703 1712 1   
 > 0 111.5  12.0

 > 12.5 1.0
 > >  >
 > >  > The first feww line of .mdp file for minimisation of
 > protein alone is
 > >  >
 > >  > ; Preprocessing
 > >  > ;
 > >  >
 > title   =  ${MOL}
 > >  >
 > cpp =  /lib/cpp;Preprocessor
 > >  >
 > define  = -DDISRES  ;For cg, and also steep
 > >  >
 > >
 > > You are not actually applying your distance restraint. 
 > If you have "#ifdef

 > > DDISRES," then you would have to "define = -DDDISRES" in the
 > .mdp file. 
 > > What

 > > you probably meant to define was "#ifdef DISRES" in the topology.
 > >
 > >  > 
 > After minimisation, the restarined residues & the adjacent

 > >  > bonds break. This results in fragmnets - residues
 > alone, peptide bond
 > >  > alone and the rest of the protein. The distance
 > restrained residues
 > >  > seems to try to move towards each other (6.04 A after
 > minimisation) and
 > >  > this might have caused fragmentation. I tried to use
 > various upper and
 > >  > lower values for bond length so as to increase
 > flexibility. But, still I
 > >  > end up in the fragments.
 > >  >
 > >
 > > Bonds don't break in classical MD, this is just an artifact of
 > > visualization,
 > > probably from nasty steric clashes within your structure.
 > >
 > >
 > >  > Some
 > of the suggestions in

[gmx-users] Re: Re: Bonds break while Minimising using distance restraints

[plmallip]

Hi,

 There is no chance of steric clashes between 6151 & 6160. They are 
seperated by 12 A. ("Warning: 1-4 interaction between 6151 and 6160 at distance 
1.387 which is larger than the 1-4 table size 1.000 nm. These are ignored for 
the rest of the simulation. This usually means your system is exploding") I 
cannot build the missing residues without knowing the secondary structure. I am 
already running one simulation with built residues. But, my ultimate goal is to 
run dynamics with distance restraints.
 
   My sytem is an pentamer. Here is the toplogy file

; Include forcefield parameters
#include "ffG43a1.itp"

; Include chain topologies
#include "chnrc_A.itp"
#include "chnrc_B.itp"
#include "chnrc_C.itp"
#include "chnrc_D.itp"
#include "chnrc_E.itp"

; Include water topology
#include "spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcx    fcy    fcz
   1    1   1000   1000   1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound    #mols
Protein_A   1
Protein_B   1
Protein_C   1
Protein_D   1
Protein_E   1
SOL  55419
NA+  54


Thanks & regards,
Latha.

> > [EMAIL PROTECTED] wrote:
> > 
> > Hi Justin, thanks for your response. You are right. I get the 
> following 
> > message in the .job file
> > 
> > "Warning: 1-4 interaction between 6151 and 6160 at distance 
> 1.387 which 
> > is larger than the 1-4 table size 1.000 nm
> > These are ignored for the rest of the simulation
> > This usually means your system is exploding"
> > 
> > The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are 
> also from 
> > the same residues). The distance between them is 12 A (there 
> are 14 
> > missing residues in between). My aim is to use distance 
> restraints, 
> > without building missing residues in between. Is there any way 
> I can 
> > overcome this warning why minimizing the system?
> 
> It's very hard to say, because none of us knows what's in your 
> system, topology, 
> or how you built things :)
> 
> You have some type of nasty steric clash that's driving atoms 
> 6151 and 6160 
> apart.  Visualize the trajectory (.trr) to see if you can 
> identify where things 
> start to break down.  I don't know if the distance 
> restraint has anything to do 
> with the problem or not.
> 
> Is there a problem with building missing residues?  That 
> might make life quite a 
> bit easier in the long run.
> 
> -Justin
> 
> > 
> > Thanks & regards,
> > Latha.
> > 
> > 
> >  > Dear colleagues,
> >  >
> >  > I need to use simple distance restraints of 12.5 A 
> between two CA atoms
> >  > of two residues. I am using the following lines in the 
> .itp file
> >  >
> >  > #ifdef DDISRES
> >  > [distance_restraints]
> >  > ;ai   aj type index type' low   
> up1  up2  fac
> >  > 1703 1712 1    
> 0 1    11.5  12.0 
> 12.5 1.0
> >  >
> >  > The first feww line of .mdp file for minimisation of 
> protein alone is
> >  >
> >  > ; Preprocessing
> >  > ;
> >  > 
> title   =  ${MOL}
> >  > 
> cpp =  /lib/cpp    ;Preprocessor
> >  > 
> define  = -DDISRES  ;For cg, and also steep
> >  >
> > 
> > You are not actually applying your distance restraint.  
> If you have "#ifdef
> > DDISRES," then you would have to "define = -DDDISRES" in the 
> .mdp file.  
> > What
> > you probably meant to define was "#ifdef DISRES" in the topology.
> > 
> >  >  
> After minimisation, the restarined residues & the adjacent
> >  > bonds break. This results in fragmnets - residues 
> alone, peptide bond
> >  > alone and the rest of the protein. The distance 
> restrained residues
> >  > seems to try to move towards each other (6.04 A after 
> minimisation) and
> >  > this might have caused fragmentation. I tried to use 
> various upper and
> >  > lower values for bond length so as to increase 
> flexibility. But, still I
> >  > end up in the fragments.
> >  >
> > 
> > Bonds don't break in classical MD, this is just an artifact of 
> > visualization,
> > probably from nasty steric clashes within your structure.
> > 
> > 
> >  > Some 
> of the suggestions in the archive says VMD doesn't show
> >  > bonds if they r above threshold value. When I checked 
> the distances
> >  > between the atoms, one of them is really long CO-CA 
> bond 3.23 A
> >  > (normally its 1.59A). This means the bond is no longer 
> there.>  >
> > 
> > No, the bond is there, VMD just isn't smart enough to see it 
> :)  You are
> > probably well on your way to an explosion if you try to 
> constrain bond 
> > lengths
> > with LINCS, however.
> > 
> > -Justin
> > 
> > 
> > ---
> -
> > 
> > ___
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://www.gromacs.org/mailma

Re: [gmx-users] Coul-SR:SOL-SOL

[Nicolas Sapay]

Nicolas Sapay wrote:

Justin A. Lemkul wrote:



Vitaly Chaban wrote:

Thank you very much!

So what energy is described by Coul-SR:SOL-SOL? And by LJ-SR?
Lennard-Jones-short range..? What is it?



I'm not 100% sure, as I've never had a need to break down energy 
terms in this level of detail, personally.  My guess would be that 
the SR contributions would come from short-range cutoffs, i.e. those 
that come from neighborsearching.  The LR contributions would be, for 
example, from PME.
The contribution of the PME to the electrostatics is called 
"Coul.-recip." in the g_energy output. AFAIR, The short-range part is 
calculated every step while the long-range part should be calculated 
every  nstlist steps. Check chapters 3 and 4 of the manual :)


Sorry, I realize I was not super clear. The contribution of the PME 
should be reparted between Coul-LJ (real space) and Coul-recip 
(reciproqual space). Coul-SR should be the contribution of pairs within 
the cutoff (rcoulomb)


Nicolas


If I've missed it, someone please correct me.

-Justin



JAL> Vitaly Chaban wrote:

Hello,

Please give me a hint what 'SR' in
Coul-SR:SOL-SOL

mean? It's in g_energy when it asks to select terms for analysis.



JAL> SR = short-range







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Re: [gmx-users] Re: Re: Bonds break while Minimising using distance restraints

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:


[EMAIL PROTECTED] wrote:

Hi Justin, thanks for your response. You are right. I get the following 
message in the .job file


"Warning: 1-4 interaction between 6151 and 6160 at distance 1.387 which 
is larger than the 1-4 table size 1.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding"

The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are also from 
the same residues). The distance between them is 12 A (there are 14 
missing residues in between). My aim is to use distance restraints, 
without building missing residues in between. Is there any way I can 
overcome this warning why minimizing the system?


It's very hard to say, because none of us knows what's in your system, topology, 
or how you built things :)


You have some type of nasty steric clash that's driving atoms 6151 and 6160 
apart.  Visualize the trajectory (.trr) to see if you can identify where things 
start to break down.  I don't know if the distance restraint has anything to do 
with the problem or not.


Is there a problem with building missing residues?  That might make life quite a 
bit easier in the long run.


-Justin



Thanks & regards,
Latha.


 > Dear colleagues,
 >
 > I need to use simple distance restraints of 12.5 A between two CA atoms
 > of two residues. I am using the following lines in the .itp file
 >
 > #ifdef DDISRES
 > [distance_restraints]
 > ;ai   aj type index type' low   up1  up2  fac
 > 1703 1712 10 111.5  12.0 12.5 1.0
 >
 > The first feww line of .mdp file for minimisation of protein alone is
 >
 > ; Preprocessing
 > ;
 > title   =  ${MOL}
 > cpp =  /lib/cpp;Preprocessor
 > define  = -DDISRES  ;For cg, and also steep
 >

You are not actually applying your distance restraint.  If you have "#ifdef
DDISRES," then you would have to "define = -DDDISRES" in the .mdp file.  
What

you probably meant to define was "#ifdef DISRES" in the topology.

 >  After minimisation, the restarined residues & the adjacent
 > bonds break. This results in fragmnets - residues alone, peptide bond
 > alone and the rest of the protein. The distance restrained residues
 > seems to try to move towards each other (6.04 A after minimisation) and
 > this might have caused fragmentation. I tried to use various upper and
 > lower values for bond length so as to increase flexibility. But, still I
 > end up in the fragments.
 >

Bonds don't break in classical MD, this is just an artifact of 
visualization,

probably from nasty steric clashes within your structure.


 > Some of the suggestions in the archive says VMD doesn't show
 > bonds if they r above threshold value. When I checked the distances
 > between the atoms, one of them is really long CO-CA bond 3.23 A
 > (normally its 1.59A). This means the bond is no longer there.
 >

No, the bond is there, VMD just isn't smart enough to see it :)  You are
probably well on your way to an explosion if you try to constrain bond 
lengths

with LINCS, however.

-Justin




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--


Justin A. Lemkul
Graduate Research Assistant
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] Visualizing g_sdf on a Mac

[Matt Wyczalkowski]

Thanks for the help.  Here is what I learned...

Yes, VMD is able to render the PLT format using the PLT Plugin:
   http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/pltplugin.html

Download the plugins at the bottom of this page:
  http://www.ks.uiuc.edu/Research/vmd/plugins/

Regards,

Matt

---
Matt Wyczalkowski
Doctoral Candidate, Biomedical Engineering
Pappu Lab: http://lima.wustl.edu
Washington University in St. Louis




On Tue, Sep 2, 2008 at 8:58 PM, Florian Dommert
<[EMAIL PROTECTED]> wrote:
> Hello,
>
>  somebode told me, that VMD is also able to render the SDF plot. However I
> have not tested it so far.
>
> Good Luck,
>
> Flo
>
> On 03.09.2008, at 01:28, Matt Wyczalkowski wrote:
>
>> I'm looking into using g_sdf for analysis.  The instructions suggest
>> using gOpenMol: "The output will be a binary 3D-grid file
>> (gom_plt.dat) in the .plt format that can be be read directly by
>> gOpenMol."
>>
>> However, the gOpenMol web site does not distribute Mac binaries (nor
>> source).  I am using Mac OS X 10.5 (ppc).
>>
>> Are gOpenMol Mac binaries available?  Or, are there alternative
>> visualization packages which would be suitable for displaying g_sdf
>> output?
>>
>> Thanks in advance for your help.
>>
>> Regards,
>>
>> Matt
>> ___
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>>
>
> --
> Florian Dommert
> Dipl.-Phys.
>
> Computational and Theoretical Softmatter & Biophysics group
>
> Frankfurt Institute for Advanced Studies
> Johann-Wolfgang-Goethe University
>
> Ruth-Moufang-Str. 1
> 60438 Frankfurt am Main
>
> Phone: +49(0)69 / 798 - 47522
> Fax:   +49(0)69 / 798 - 47611
>
> EMail: [EMAIL PROTECTED]
> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
>
>
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Re: [gmx-users] Coul-SR:SOL-SOL

[Nicolas Sapay]

Justin A. Lemkul wrote:



Vitaly Chaban wrote:

Thank you very much!

So what energy is described by Coul-SR:SOL-SOL? And by LJ-SR?
Lennard-Jones-short range..? What is it?



I'm not 100% sure, as I've never had a need to break down energy terms 
in this level of detail, personally.  My guess would be that the SR 
contributions would come from short-range cutoffs, i.e. those that 
come from neighborsearching.  The LR contributions would be, for 
example, from PME.
The contribution of the PME to the electrostatics is called 
"Coul.-recip." in the g_energy output. AFAIR, The short-range part is 
calculated every step while the long-range part should be calculated 
every  nstlist steps. Check chapters 3 and 4 of the manual :)




If I've missed it, someone please correct me.

-Justin



JAL> Vitaly Chaban wrote:

Hello,

Please give me a hint what 'SR' in
Coul-SR:SOL-SOL

mean? It's in g_energy when it asks to select terms for analysis.



JAL> SR = short-range







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n:SAPAY;Nicolas
org:University of Calgary;Biological Sciences
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
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[gmx-users] Re: Re: Bonds break while Minimising using distance restraints

[plmallip]

[EMAIL PROTECTED] wrote:

Hi Justin, thanks for your response. You are right. I get the following message 
in the .job file

"Warning: 1-4 interaction between 6151 and 6160 at distance 1.387 which is 
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding"

The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are also from the 
same residues). The distance between them is 12 A (there are 14 missing 
residues in between). My aim is to use distance restraints, without building 
missing residues in between. Is there any way I can overcome this warning why 
minimizing the system?

Thanks & regards,
Latha.


> Dear colleagues,
>
> I need to use simple distance restraints of 12.5 A between two CA atoms
> of two residues. I am using the following lines in the .itp file
>
> #ifdef DDISRES
> [distance_restraints]
> ;ai   aj type index type' low   up1  up2  fac
> 1703 1712 1    0 1    11.5  12.0 12.5 1.0
>
> The first feww line of .mdp file for minimisation of protein alone is
>
> ; Preprocessing
> ;
> title   =  ${MOL}
> cpp =  /lib/cpp    ;Preprocessor
> define  = -DDISRES  ;For cg, and also steep
>

You are not actually applying your distance restraint.  If you have "#ifdef
DDISRES," then you would have to "define = -DDDISRES" in the .mdp file.  What
you probably meant to define was "#ifdef DISRES" in the topology.

>  After minimisation, the restarined residues & the adjacent
> bonds break. This results in fragmnets - residues alone, peptide bond
> alone and the rest of the protein. The distance restrained residues
> seems to try to move towards each other (6.04 A after minimisation) and
> this might have caused fragmentation. I tried to use various upper and
> lower values for bond length so as to increase flexibility. But, still I
> end up in the fragments.
>

Bonds don't break in classical MD, this is just an artifact of visualization,
probably from nasty steric clashes within your structure.


> Some of the suggestions in the archive says VMD doesn't show
> bonds if they r above threshold value. When I checked the distances
> between the atoms, one of them is really long CO-CA bond 3.23 A
> (normally its 1.59A). This means the bond is no longer there.
>

No, the bond is there, VMD just isn't smart enough to see it :)  You are
probably well on your way to an explosion if you try to constrain bond lengths
with LINCS, however.

-Justin

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[gmx-users] Glycam and gromacs

[Serena Leone]

Hello everybody,

I would just like to renew a question that was made more or less one 
year ago and that received no answer: Has anyone tried (and 
succeeded...) to use Glycam (with Amber ff) in Gromacs?


Thank you,

Cheers,
Serena
--

Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel)  617-732-8586






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Re: Re: [gmx-users] how to make h-bond existence map?

[minnale]

  
Thanks to Florain for prompt reply
May be this is trivial query to you
I have done in this way
1. Making index file 
  make_ndx -f .gro -o .ndx
  selected 7(mainchain+H)& r 24 26 45 67 78
  the index showed like this
  [ MainChain+H_&_r_22_50_56_121_22 ]
 370  370  371  371  372  372  386  386  387  387  822  823  824  838  839
 916  917  918  932  933 1839 1840 1841 1855 1856

2. g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm .xpm -r 0.35 -a 30
   it showed 
 Select a group: 15
 Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
 Select a group: 15
 Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
 Calculating hydrogen bonds in MainChain+H_&_r_22_50_56_121_22 (25
 atoms) Found 4 donors and 8 acceptors
 Reading frame 0 time 0.000
 Will do grid-seach on 16x16x16 grid, rcut=0.35
 Reading frame   37000 time 7400.000
 No hydrogen bonds found!!
 Average number of hbonds per timeframe 0.000 out of 16 possible
 
  Then I have given same command but slight change -r 0.25 -a 30 but it showed 
same data I have pasted above tells no H-bonds found.
 
Could please suggest me angle cutoff and radius cutoff values.I have tried to 
get information about these values but I couldnt able to get.

Thanks in advance

On Wed, 03 Sep 2008 Florian Haberl wrote :
>Hi,
>
>On Wednesday, 3. September 2008, minnale wrote:
> > Thanks Florian for your detailed reply
> > when I mentioned -r and -a options in g_hbond command its showing
> >  Fatal error:
> > Expected a real argument for option -a
> > similar error showing when I mentioned cutoff radius(-r) or cutoffangle
> > (-a)
> > Could you please suggest me
> > Thanks in advance.
>
>try
>
>g_hbond -h
>
>You must enter other values, but be careful the default options are normally
>the standard onces.
>
>Take also a look on your structure, if all residues you want to analyse are in
>your index group!
>
>Greetings,
>
>Florian
>
>
> >
> > On Wed, 03 Sep 2008 Florian Haberl wrote :
> > >Hi,
> > >
> > >On Wednesday, 3. September 2008, minnale wrote:
> > > > Thanks Justin for your valuable suggestions
> > > > I have done the way you suggested. I gave command like this
> > > > g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms)
> > > > -num .xvg -hbm .xpm it showed
> > > > Select a group: 15
> > > > Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
> > > > Select a group: 15
> > > > Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
> > > > Calculating hydrogen bonds in MainChain+H_&_r_22_50_56_121_22 (25
> > > > atoms) Found 4 donors and 8 acceptors
> > > > Reading frame   0 time0.000
> > > > Will do grid-seach on 16x16x16 grid, rcut=0.35
> > > > Reading frame   37000 time 7400.000
> > > > No hydrogen bonds found!!
> > > > Average number of hbonds per timeframe 0.000 out of 16 possible
> > > >
> > > > gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey)
> > > >
> > > > It displayed there is no Hydrogen bonds in selected mainchain+H
> > > > residues. but it showed 4 donors and 8 acceptors, that doesnt mean that
> > > > its having H-bond? Later
> > >
> > >This means that only in principle there are donors and acceptors around
> > > but if the distance or angle is not correct than g_hbond will not find
> > > any (formed) hbond.
> > >
> > >you can try g_hbond with the option -r and -a to change cutoff radius and
> > >cutoff angle but this are the standard criteria for an h-bond.
> > >
> > >greetings,
> > >
> > >Florian
> > >
> > > > when I tried to convert .xpm to .eps by using command
> > > > xpm2ps -f .xpm -o .eps it showed
> > > > Floating point exception
> > > > Can you please give me your kind suggestion
> > > >
> > > > Thanks in advance.
> > > >
> > > > On Wed, 03 Sep 2008 Justin A.Lemkul wrote :
> > > > >minnale wrote:
> > > > >>  Hi all,
> > > > >>   I am confusing while calculating hydrogen bonds of my protein.I
> > > > >> issued this command g_hbond -f .xtc -s .tpr -num .xvg I didnt
> > > > >> mention .ndx because I wanted to know the H-bonds in whole protein
> > > > >> system. I have selected mainchain+H two times, command went fine and
> > > > >> it showed
> > > > >>
> > > > >>Select a group: 7
> > > > >>Selected 7: 'MainChain+H'
> > > > >>Select a group: 7
> > > > >>Selected 7: 'MainChain+H'
> > > > >>Calculating hydrogen bonds in MainChain+H (881 atoms)
> > > > >>Found 170 donors and 355 acceptors
> > > > >>Reading frame  0 time0.000 Will do grid-seach on 16x16x16
> > > > >> grid, rcut=0.35 Reading frame  37000 time 7400.000 Average number of
> > > > >> hbonds per timeframe 81.692 out of 30175 possible gcq#295: "It Just
> > > > >> Tastes Better" (Burger King)
> > > > >>
> > > > >>It generated .xvg file and it con@title "Hydrogen Bonds"
> > > > >>@xaxis  label "Time"
> > > > >>@yaxis  label "Number"
> > > > >>@TYPE xy
> > > > >>@ view 0.15, 0.15, 0.75, 0.85
> > > > >>@ legend on
> > > > >>@ legend box on
> > > > >>@ legend loctype view
> > > > >>@ legend 0.78, 0.8
> > > > >>@ legend length 2
> > > > >>@ s0 legend "Hydrogen bonds"
> > > > >>@ 

Re: [gmx-users] Parameters for DNA bases

[TJ Piggot]

If you really want to use OPLS/AA then you can find DNA parameters on the 
Gromacs website using the following link.


http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,45/Itemid,26/

However i am not sure that these parameters are well tested and i am not 
sure if they have been used in many/any published works. Like Justin said 
the AMBER forcefields would be a better option unless you need OPLS/AA for 
a specific reason, for more info on the AMBER forcefields in Gromacs see:


http://chemistry.csulb.edu/ffamber/

Hope this helps

Tom

--On Tuesday, September 02, 2008 21:24:45 -0400 "Justin A. Lemkul" 
<[EMAIL PROTECTED]> wrote:





Jeff Woodford wrote:

Hi all,

Forgive me if this is a stupid question, but:

I am attempting to simulate the interaction between a peptide and a DNA
strand using the OPLS/AA force field.  However the parameters for the
DNA bases don't appear to be included.  Where might I find these
parameters suitable for adapting to GROMACS?




Any particular motivation for using OPLS-AA?  The AMBER force fields
include both DNA and protein.

-Justin



Thanks in advance,

-Jeff



Jeffrey N. Woodford

Associate Professor of Chemistry

Eastern Oregon University

Tel: 541-962-3321

Fax: 541-962-3873






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Justin A. Lemkul
Graduate Research Assistant
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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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.

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Re[2]: [gmx-users] Coul-SR:SOL-SOL

[Vitaly Chaban]

JAL> I'm not 100% sure, as I've never had a need to break down energy terms in 
this
JAL> level of detail, personally.

Me too. :)

JAL>  My guess would be that the SR contributions would
JAL> come from short-range cutoffs, i.e. those that come from 
neighborsearching.  The
JAL> LR contributions would be, for example, from PME.

I think you are right about it. Let it be so. I've understood what
term I wanted now.

JAL> Vitaly Chaban wrote:
>> Thank you very much!
>> 
>> So what energy is described by Coul-SR:SOL-SOL? And by LJ-SR?
>> Lennard-Jones-short range..? What is it?
>> 



>> 
>> JAL> Vitaly Chaban wrote:
 Hello,

 Please give me a hint what 'SR' in
 Coul-SR:SOL-SOL

 mean? It's in g_energy when it asks to select terms for analysis.

>> 
>> JAL> SR = short-range
>> 
>> 
>> 






-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban

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Re: [gmx-users] Bonds missing in VMD visualization [SOLVED]

[Andreas Kring]

Thank you for solution suggestions!

Solution 1 worked out just fine. After a little Goolgeing it seemed as 
if solution 2 requires modification of the VMD source code. Solution 3 
also looks attractive - I'll have a closer look at this later on...


/Andreas

Diego Enry skrev:

So I was testing on VMD the C-CL bond distance to draw a bond.
Actually, the limit was a disturbing 1.80A ! So close to the 1.81A you
need :(

Solutions !

1) Use "dynamic bonds representation" and set the cut-off to 1.81 or more

2) Find where VMD sets it's standard cutoff for bonds and set it to
1.81 or more forever.

3) VMD FAQ solution is to make a .PSF (topology) to solve this
problem. ( You will only need the bond list )
http://www.ks.uiuc.edu/Research/vmd/allversions/vmd_faq.html

How to write a .PSF file
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html


On Tue, Sep 2, 2008 at 5:59 AM, Andreas Kring <[EMAIL PROTECTED]> wrote:

Thank you for your reply. I tried the following:


VMD computes distances between pairs of atoms to "draw" a bond. So I
think your atoms are too distanced from each other.
Check the bond distribution during MD and compare with your topology.
C-CL should be around 1.76A.

In 1,1,1-trichloroethane the C-Cl bond distance should be around 1.81A. I
checked the C-Cl bond distances using g_bond and this give a nice Gaussian
distribution around 1.81A (which matches what is in the topology file).


VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb
you open before the .xtc/.trr), this distance is greater than 2.0A.

All bond distances are less than 2.0A, but VMD still does not draw a bond?

Is there anything else I can try?

/Andreas
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--
##

Andreas Kring, Ph.D.-student
University of Copenhagen
Niels Bohr Institute
Universitetsparken 5
DK-2100 Copenhagen
Denmark

Phone
  Office (D304): (+45) 35 32 04 91
  Home:  (+45) 77 42 55 78
  Mobile:(+45) 61 77 55 78

E-mail: [EMAIL PROTECTED]
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Re: [gmx-users] Coul-SR:SOL-SOL

[Justin A. Lemkul]

Vitaly Chaban wrote:

Thank you very much!

So what energy is described by Coul-SR:SOL-SOL? And by LJ-SR?
Lennard-Jones-short range..? What is it?



I'm not 100% sure, as I've never had a need to break down energy terms in this 
level of detail, personally.  My guess would be that the SR contributions would 
come from short-range cutoffs, i.e. those that come from neighborsearching.  The 
LR contributions would be, for example, from PME.


If I've missed it, someone please correct me.

-Justin



JAL> Vitaly Chaban wrote:

Hello,

Please give me a hint what 'SR' in
Coul-SR:SOL-SOL

mean? It's in g_energy when it asks to select terms for analysis.



JAL> SR = short-range





--


Justin A. Lemkul
Graduate Research Assistant
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] Coul-SR:SOL-SOL

[Xavier Periole]

On Wed, 3 Sep 2008 12:43:14 +0300
 Vitaly Chaban <[EMAIL PROTECTED]> wrote:

Hello,

Please give me a hint what 'SR' in

SR: short-range
LR: long-range

Coul-SR:SOL-SOL

mean? It's in g_energy when it asks to select terms for analysis.

Is it a Coulomb term of interaction among SOL particles? And what's
then 'rest' in
Coul-SR:SOL-rest

Is it 'rest' for all other groups not defined in .mdp as energy groups?

Thanks.

--
Vitaly

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-
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-
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Re: [gmx-users] Coul-SR:SOL-SOL

[Justin A. Lemkul]

Vitaly Chaban wrote:

Hello,

Please give me a hint what 'SR' in
Coul-SR:SOL-SOL

mean? It's in g_energy when it asks to select terms for analysis.



SR = short-range


Is it a Coulomb term of interaction among SOL particles? And what's
then 'rest' in
Coul-SR:SOL-rest

Is it 'rest' for all other groups not defined in .mdp as energy groups?



I believe so, yes.

-Justin


Thanks.

--
Vitaly

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--


Justin A. Lemkul
Graduate Research Assistant
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] Problems with molecular dynamic investigation of an cyclic peptide nanotube

[Justin A. Lemkul]

huifang liu wrote:

Hi, Gromacs users,
 
I was caught by a big problem with molecular dynamic investigation of an 
cyclic peptide nanotube. When i do energy minimization with em.mdp 
parameter file as follows, it gave out a warning: Warning: 1-4 
interaction between 135 and 144 at distance larger than 1 nm. I 
ignored it and went on the next step with pr.mdp as follows, but it 
crashed with the following information:
 


Your system is exploding.  Have a look here:

http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off

as well as:

http://wiki.gromacs.org/index.php/blowing_up

-Justin



Wrote pdb files with previous and current coordinates

[node1:15777] *** Process received signal ***

[node1:15777] Signal: Segmentation fault (11)

[node1:15777] Signal code: Address not mapped (1)

[node1:15777] Failing at address: 0xba8e28

[node1:15777] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0]

[node1:15777] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58]

[node1:15777] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97]

[node1:15777] [ 3] mdrun_ompi(force+0x120) [0x4432f0]

[node1:15777] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb]

[node1:15777] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf]

[node1:15777] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc]

[node1:15777] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd]

[node1:15777] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x307851c3fb]


[node1:15777] [ 9] mdrun_ompi [0x412e8a]

[node1:15777] *** End of error message ***

Segmentation fault

 

I am extremely puzzed and don't know how to solve this problem. In 
additon, my previous system runs normally with the same parameter file. 

 


##em.mdp file

cpp =  /lib/cpp
define  =  -DPOSRES
constraints =  none
integrator  =  steep
nsteps  =  100
;
;   Energy minimizing stuff
;
emtol   =  2000
emstep  =  0.01

nstcomm =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no

 

 

 


#pr.mdp

title   =  Yo
cpp =  /lib/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  2500  ; total 5 ps.
nstcomm =  1
nstxout =  500
nstvout =  1000
nstfout =  0
nstlog  =  500
nstenergy   =  500
nstlist =  5
ns_type =  grid
coulombtype =  PME
rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
fourierspacing  =  0.12
pme_order   =  4
optimize_fft=  yes
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc-grps =   Protein
tau_t   =   0.1
ref_t   =10
; Energy monitoring
energygrps  =  Protein
; Pressure coupling is not on
Pcoupl  =  berendsen
pcoupltype  =  anisotropic
tau_p   =  1
compressibility =  4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p   =  1 1 1 1 1 1
; Generate velocites is on at 300 K.
gen_vel =  no
gen_temp=  300.0
gen_seed=  173529

 

 


Look forward to your help. Thanks in advance.

 

Huifang 

 





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--


Justin A. Lemkul
Graduate Research Assistant
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] Coul-SR:SOL-SOL

[Vitaly Chaban]

Hello,

Please give me a hint what 'SR' in
Coul-SR:SOL-SOL

mean? It's in g_energy when it asks to select terms for analysis.

Is it a Coulomb term of interaction among SOL particles? And what's
then 'rest' in
Coul-SR:SOL-rest

Is it 'rest' for all other groups not defined in .mdp as energy groups?

Thanks.

--
Vitaly

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[gmx-users] Re[4]: Using Morse potentials with ENCAD force field

[Vitaly Chaban]

1NIT N11  -0.552   0.004  -0.026
1NIT N22   0.552  -0.004   0.026
  2.0  2.0  1.2

Andy,

If I were your system, I would explode immediately and never let run myself 
again.


b0 (N-N) = (0.552+0.552)=1.104 nm. How should the system behave with such 
unrealistic solvent and huge energies respectively?


AS> Vitaly,
AS> 
AS> Attached is all the files for my forcefield.  In ffgmxnb.itp there are two 
sets of data used for C-N, C-O, and O-N.  One set of data is from literature I 
found and is commented out.  The other is from combining like in the gromacs 
manual with the values given from the ffgmxnb.itp file. Thanks for the help.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban

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Re: [gmx-users] how to make h-bond existence map?

[Florian Haberl]

Hi,

On Wednesday, 3. September 2008, minnale wrote:
> Thanks Florian for your detailed reply
> when I mentioned -r and -a options in g_hbond command its showing
>  Fatal error:
> Expected a real argument for option -a
> similar error showing when I mentioned cutoff radius(-r) or cutoffangle
> (-a)
> Could you please suggest me
> Thanks in advance.

try 

g_hbond -h 

You must enter other values, but be careful the default options are normally 
the standard onces.

Take also a look on your structure, if all residues you want to analyse are in 
your index group!

Greetings,

Florian


>
> On Wed, 03 Sep 2008 Florian Haberl wrote :
> >Hi,
> >
> >On Wednesday, 3. September 2008, minnale wrote:
> > > Thanks Justin for your valuable suggestions
> > > I have done the way you suggested. I gave command like this
> > > g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms) 
> > > -num .xvg -hbm .xpm it showed
> > > Select a group: 15
> > > Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
> > > Select a group: 15
> > > Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
> > > Calculating hydrogen bonds in MainChain+H_&_r_22_50_56_121_22 (25
> > > atoms) Found 4 donors and 8 acceptors
> > > Reading frame   0 time0.000
> > > Will do grid-seach on 16x16x16 grid, rcut=0.35
> > > Reading frame   37000 time 7400.000
> > > No hydrogen bonds found!!
> > > Average number of hbonds per timeframe 0.000 out of 16 possible
> > >
> > > gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey)
> > >
> > > It displayed there is no Hydrogen bonds in selected mainchain+H
> > > residues. but it showed 4 donors and 8 acceptors, that doesnt mean that
> > > its having H-bond? Later
> >
> >This means that only in principle there are donors and acceptors around
> > but if the distance or angle is not correct than g_hbond will not find
> > any (formed) hbond.
> >
> >you can try g_hbond with the option -r and -a to change cutoff radius and
> >cutoff angle but this are the standard criteria for an h-bond.
> >
> >greetings,
> >
> >Florian
> >
> > > when I tried to convert .xpm to .eps by using command
> > > xpm2ps -f .xpm -o .eps it showed
> > > Floating point exception
> > > Can you please give me your kind suggestion
> > >
> > > Thanks in advance.
> > >
> > > On Wed, 03 Sep 2008 Justin A.Lemkul wrote :
> > > >minnale wrote:
> > > >>  Hi all,
> > > >>   I am confusing while calculating hydrogen bonds of my protein.I
> > > >> issued this command g_hbond -f .xtc -s .tpr -num .xvg I didnt
> > > >> mention .ndx because I wanted to know the H-bonds in whole protein
> > > >> system. I have selected mainchain+H two times, command went fine and
> > > >> it showed
> > > >>
> > > >>Select a group: 7
> > > >>Selected 7: 'MainChain+H'
> > > >>Select a group: 7
> > > >>Selected 7: 'MainChain+H'
> > > >>Calculating hydrogen bonds in MainChain+H (881 atoms)
> > > >>Found 170 donors and 355 acceptors
> > > >>Reading frame  0 time0.000 Will do grid-seach on 16x16x16
> > > >> grid, rcut=0.35 Reading frame  37000 time 7400.000 Average number of
> > > >> hbonds per timeframe 81.692 out of 30175 possible gcq#295: "It Just
> > > >> Tastes Better" (Burger King)
> > > >>
> > > >>It generated .xvg file and it con@title "Hydrogen Bonds"
> > > >>@xaxis  label "Time"
> > > >>@yaxis  label "Number"
> > > >>@TYPE xy
> > > >>@ view 0.15, 0.15, 0.75, 0.85
> > > >>@ legend on
> > > >>@ legend box on
> > > >>@ legend loctype view
> > > >>@ legend 0.78, 0.8
> > > >>@ legend length 2
> > > >>@ s0 legend "Hydrogen bonds"
> > > >>@ s1 legend "Pairs within 0.35 nm"
> > > >> 0  79674
> > > >>   0.2  87687
> > > >>   0.4  80693
> > > >> .
> > > >> .
> > > >> .
> > > >>   .
> > > >>   .
> > > >> etc
> > > >>
> > > >>1.Could you please tell me the way I have done was correct or not?
> > > >
> > > >For calculating H-bonds within the MainChain, yes.  You have not
> > > > determined all of the H-bonds in the protein, however, because you
> > > > are not including side chains in the calculation.
> > > >
> > > >>2. how can I make h-bond existence map?
> > > >
> > > >Is g_hbond -hbm not what you want?
> > > >
> > > >-Justin
> > > >
> > > >>3. For this is it require to write programming or script?
> > > >>
> > > >>
> > > >>
> > > >>Rediff Shopping
> > > >>  > > >>sign
> > > >> ature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201650/1?PARTNER=
> > > >>3&OAS _QUERY=null>
> > > >>
> > > >>
> > > >>-
> > > >>---
> > > >>
> > > >>___
> > > >>gmx-users mailing listgmx-users@gromacs.org
> > > >>http://www.gromacs.org/mailman/listinfo/gmx-users
> > > >>Please search the archive at http://www.gromacs.org/search before
> > > >> posting! Please don't post (un)subscribe requ

Re: Re: [gmx-users] how to make h-bond existence map?

[minnale]

  
Thanks Florian for your detailed reply 
when I mentioned -r and -a options in g_hbond command its showing
 Fatal error:
Expected a real argument for option -a
similar error showing when I mentioned cutoff radius(-r) or cutoffangle
(-a)
Could you please suggest me
Thanks in advance.
On Wed, 03 Sep 2008 Florian Haberl wrote :
>Hi,
>
>On Wednesday, 3. September 2008, minnale wrote:
> > Thanks Justin for your valuable suggestions
> > I have done the way you suggested. I gave command like this
> > g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms)  -num
> > .xvg -hbm .xpm it showed
> > Select a group: 15
> > Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
> > Select a group: 15
> > Selected 15: 'MainChain+H_&_r_22_50_56_121_22'
> > Calculating hydrogen bonds in MainChain+H_&_r_22_50_56_121_22 (25 atoms)
> > Found 4 donors and 8 acceptors
> > Reading frame   0 time0.000
> > Will do grid-seach on 16x16x16 grid, rcut=0.35
> > Reading frame   37000 time 7400.000
> > No hydrogen bonds found!!
> > Average number of hbonds per timeframe 0.000 out of 16 possible
> >
> > gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey)
> >
> > It displayed there is no Hydrogen bonds in selected mainchain+H residues.
> > but it showed 4 donors and 8 acceptors, that doesnt mean that its having
> > H-bond? Later
>
>This means that only in principle there are donors and acceptors around but if
>the distance or angle is not correct than g_hbond will not find any (formed)
>hbond.
>
>you can try g_hbond with the option -r and -a to change cutoff radius and
>cutoff angle but this are the standard criteria for an h-bond.
>
>greetings,
>
>Florian
>
> > when I tried to convert .xpm to .eps by using command
> > xpm2ps -f .xpm -o .eps it showed
> > Floating point exception
> > Can you please give me your kind suggestion
> >
> > Thanks in advance.
> >
> > On Wed, 03 Sep 2008 Justin A.Lemkul wrote :
> > >minnale wrote:
> > >>  Hi all,
> > >>   I am confusing while calculating hydrogen bonds of my protein.I issued
> > >> this command g_hbond -f .xtc -s .tpr -num .xvg I didnt mention .ndx
> > >> because I wanted to know the H-bonds in whole protein system. I have
> > >> selected mainchain+H two times, command went fine and it showed
> > >>
> > >>Select a group: 7
> > >>Selected 7: 'MainChain+H'
> > >>Select a group: 7
> > >>Selected 7: 'MainChain+H'
> > >>Calculating hydrogen bonds in MainChain+H (881 atoms)
> > >>Found 170 donors and 355 acceptors
> > >>Reading frame  0 time0.000 Will do grid-seach on 16x16x16 grid,
> > >> rcut=0.35 Reading frame  37000 time 7400.000 Average number of hbonds
> > >> per timeframe 81.692 out of 30175 possible gcq#295: "It Just Tastes
> > >> Better" (Burger King)
> > >>
> > >>It generated .xvg file and it con@title "Hydrogen Bonds"
> > >>@xaxis  label "Time"
> > >>@yaxis  label "Number"
> > >>@TYPE xy
> > >>@ view 0.15, 0.15, 0.75, 0.85
> > >>@ legend on
> > >>@ legend box on
> > >>@ legend loctype view
> > >>@ legend 0.78, 0.8
> > >>@ legend length 2
> > >>@ s0 legend "Hydrogen bonds"
> > >>@ s1 legend "Pairs within 0.35 nm"
> > >> 0  79674
> > >>   0.2  87687
> > >>   0.4  80693
> > >> .
> > >> .
> > >> .
> > >>   .
> > >>   .
> > >> etc
> > >>
> > >>1.Could you please tell me the way I have done was correct or not?
> > >
> > >For calculating H-bonds within the MainChain, yes.  You have not
> > > determined all of the H-bonds in the protein, however, because you are
> > > not including side chains in the calculation.
> > >
> > >>2. how can I make h-bond existence map?
> > >
> > >Is g_hbond -hbm not what you want?
> > >
> > >-Justin
> > >
> > >>3. For this is it require to write programming or script?
> > >>
> > >>
> > >>
> > >>Rediff Shopping
> > >>  > >>ature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201650/1?PARTNER=3&OAS
> > >>_QUERY=null>
> > >>
> > >>
> > >>
> > >>
> > >>___
> > >>gmx-users mailing listgmx-users@gromacs.org
> > >>http://www.gromacs.org/mailman/listinfo/gmx-users
> > >>Please search the archive at http://www.gromacs.org/search before
> > >> posting! Please don't post (un)subscribe requests to the list. Use the
> > >> www interface or send it to [EMAIL PROTECTED] Can't post?
> > >> Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > >-- 
> > >
> > >Justin A. Lemkul
> > >Graduate Research Assistant
> > >Department of Biochemistry
> > >Virginia Tech
> > >Blacksburg, VA
> > >jalemkul[at]vt.edu | (540) 231-9080
> > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > >
>
>
>
>--
>---