[gmx-users] how to constrain water with SETTLE

2008-07-07 Thread 火枪手 
In gromacs how i could use SETTLE to constrain water? I can't find this 
option.Please help me.___
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[gmx-users] Accuracy of force calculation and doubts on PME parameter choice

2008-07-07 Thread Nickle Fan 
Dear all:

In most studies, we focus on the accuracy of potential energy. How about the
force? Consider two systems:

1. Two LJ particles (sigma=0.33nm, epsilon=0.625kJ/mol): If the force is
cutoff at 2.5*sigma, so the maximum error in force is at the cutoff length
and equal to ~0.08 kJ/mol nm.

2. Two point charges in a 3*3*3.3nm box (charge separation: 0.5 nm, q1=e,
q2=-e): I tried the following calculations:
a. Ewald summation, rcutoff=1.0nm, ewald_tol=1e-5, FFT_spacing=0.1nm: This
produces: f1=-f2=542.2 kJ/mol nm;
b. PME, rcutoff=1.0 nm, ewald_tol=1e-5; 4th order, FFT_spacing=0.1nm, this
produces: f1=-f2=543.9 kJ/mol nm;
c. PME, rcutoff=1.0 nm, ewald_tol=1e-5; 4th order, FFT_spacing=0.11nm, this
produces: f1=543.97 kJ/mol nm, f2=-544.96 kJ/mol nm;
d. PME, rcutoff=1.0 nm, ewald_tol=1e-5; 4th order, FFT_spacing=0.12nm, this
produces: f1=543.43 kJ/mol nm, f2=-545.49 kJ/mol nm;

Clearly, for LJ particles, the maximum accuracy is ~0.08kJ/mol nm - which
sounds small. But for electrostatics, the error is quite large: if we take
the Ewald results to be the exact solution, then for choice d (which seems
to be a popular choice among gmx-users), the error amounts to be ~ 2.0
kJ/mol nm. Is this error acceptable?

Thanks for your time.

Nick
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Re: [gmx-users] Error:Cannot determine precision of trn file

2008-07-07 Thread Justin A. Lemkul 

What does gmxcheck tell you about these .trr files?

Also, it is better to give exact command lines with copy-pasted screen 
output, instead of leaving us to guess at what you're trying.


-Justin

[EMAIL PROTECTED] wrote:

Dear colleagues,

  I successfully finished a 3 ns gromacs run using 40 
nodes.  When, I tried to convert .trr file to .xtc using trjconv, the 
run stops at 560 frame giving error "cannot determimine precision of 
trn file". I tried various options like -skip, -b and -e, -dt option 
as well as -ndx option . But, each time, the run stops at 560. 
The second run I gave for 6 ns and this time, the 
trjconv stops at 1180 frame. I have observed the .trr files occupying 
huge memory space - 18 G for 3ns and 34 G for 6 ns runs respectively. 
Memory is not a problem, as I have lot of disk space available.
  My system is a pentamer with 1052 residues and 47201 water 
molecules.The simulation ran for 5 days.


I would be extremely thankful for any kind of suggestions in this regard.

Prema,
Graduate student,
University of Houston.


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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] Error:Cannot determine precision of trn file

2008-07-07 Thread plmallip 
Dear colleagues,

  I successfully finished a 3 ns gromacs run using 40 nodes.  
When, I tried to convert .trr file to .xtc using trjconv, the run stops at 560 
frame giving error "cannot determimine precision of trn file". I tried various 
options like -skip, -b and -e, -dt option as well as -ndx option . But, each 
time, the run stops at 560.  
    The second run I gave for 6 ns and this time, the trjconv stops 
at 1180 frame. I have observed the .trr files occupying huge memory space - 18 
G for 3ns and 34 G for 6 ns runs respectively. Memory is not a problem, as I 
have lot of disk space available.
  My system is a pentamer with 1052 residues and 47201 water molecules.The 
simulation ran for 5 days.

I would be extremely thankful for any kind of suggestions in this regard.

Prema,
Graduate student,
University of Houston.

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Re: [gmx-users] rot_diff

2008-07-07 Thread rams rams 
Dear XAvier,

Thanks for your reply and for the explanation. I am not an NMR guy so I
would like to know little bit of more about the way we can calculate the
rotational diffusion. The way I understood is the following and let me know
if I am wrong.

After obtaining the rotaional correlation function using Gromacs tools
(g_rotacf), I need to calculate the correlation time I suppose.
The obtained correlation time is related with the local diffusion constant
(d) by the relation
d = 1/l(l+1) t
t is the correlation time obtained above and l = 1 or 2 depends upon the
order of the legendre polynomial we will use in the g_rotacf and the
experimental results with which we are comparing.

then by solving the following relation
d=n'Qn (n is a unit vector lies along the vector connecting the two spins),
we can obtain "Q" which inturn is in relation with D (the diffusion tensor).


Thats the overall idea I have but I am sure I need to worry alot of finer
other details while I start putting my hands into it. If the overall idea is
alright I could put the things in a more detailed way.

Ram.

On Sat, Jul 5, 2008 at 12:51 PM, Xavier Periole <[EMAIL PROTECTED]> wrote:

> On Sat, 5 Jul 2008 10:40:21 -0400
>  "rams rams" <[EMAIL PROTECTED]> wrote:
>
>> Dear users,
>>
>> Is it possible to evaluate the rotational diffusion of proteins using
>> gromacs tools ??
>>
> No directly. However you can use g_rotacf to generate the autocorrelation
> function of vectors (option -d). By defining vectors representing your
> molecule/protein you can access the rotational correlation time of your
> representative vector. You can imagine different way to get a statistically
> significant value. One would be to define many vectors between backbone
> atoms and average your results. Another would be to again define many
> vectors but this time between the center of mass of the protein and each
> Ca atoms and average ...
>
> You can also hack the g_rms code to extract the rotational matrix during
> the overlay of your protein to a reference structure and apply it to
> a unit vector from whose trajectory you can again use g_rotacf to get
> the autocorrelation function of that vector ...
>
> An important point in the comparison of your result to experimental
> values is the way the rotational correlation time is extracted
> experimentally. They select different mode of relaxation (1 or 2) and thus
> you have to use the corresponding Legendre polynomial when calculating the
> autocorrelation function. From NMR relaxation l=2.
>
> XAvier.
>
> -
> XAvier Periole - PhD
>
> Molecular Dynamics Group
> - NMR and Computation -
> University of Groningen
> The Netherlands
> -
> ___
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Re: [gmx-users] simulating two peptides in a box

2008-07-07 Thread Justin A. Lemkul 



kartik mehra wrote:


Dear Justin,

1. They are the same protein ( 2 copies of the same protein)



OK, that makes life a little easier :-)

2. The order in the .gro file seems fine... Basically it lists the 
co-ordinates of a single copy of  peptide and then the solvent 
molecule ... I presume since the .top file has 4 copies of the same 
molecule, this is how the .gro file should look ?


That's the problem.  Everything that's in the .top file must be in the 
.gro file.  Therefore, if you have 4 copies of your protein, you *must* 
provide the coordinates for four copies of the protein in the .gro 
file.  Otherwise, how does mdrun know where they are to do any 
calculations? 



3. Also is there an easier way of dealing with the modification of 
number of solvent molecules ( since the co-ordinates involve a factor 
of 3 arising out of the description of SPC atoms ... )




When you run genbox, use the -p flag, giving the name of your topology 
file.  It will modify the [ molecules ] section to add the number of 
water molecules it placed in your system.  Otherwise, genbox prints out 
how many water molecules it added, and you can type them in yourself.  
Not terribly laborious, either way, really.


-Justin






Thanks




-
From: *Justin A. Lemkul* <[EMAIL PROTECTED] >
Date: Mon, Jul 7, 2008 at 11:30 AM
Subject: Re: [gmx-users] simulating two peptides in a box
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>




kartik mehra wrote:


   Dear Gromacs USers


1. Please disregard the previous mail which was sent from a
different email id 

2. I have copied the relevant portion here ...( previous mail
had a wrong command ...I have copied the actual command here)

Dear Justin,

 Here is the exact error message : ( Here I have tried to
simulate 4 protein molecules in a box ...basically I am
looking at multiple molecule interactions )

*grompp  -f em.mdp -c nt17_sol.gro -o nt17_em.tpr -p nt17.top*

*checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 4
Excluding 2 bonded neighbours for SOL 8813
NOTE:
 System has non-zero total charge: 4.00e+00

processing coordinates...
Warning: atom names in nt17.top and nt17_sol.gro don't match
(N - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(H1 - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(H2 - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(H3 - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(CG - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(SD - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(CE - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match
(CA - HW1)
(more than 20 non-matching atom names)
WARNING 1 [file "nt17.top", line 1126]:
 534 non-matching atom names
 atom names from nt17.top will be used
 atom names from nt17_sol.gro will be ignored

double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#  BONDS:   17626
#   G96BONDS:   716
# ANGLES:   8813
#  G96ANGLES:   1040
#  PDIHS:   372
#  IDIHS:   320
#   LJ14:   1104
initialising group options...
processing index file...
Analysing residue names:
Opening library file
/usr/local/gromacs/3.3.1/64/gnu/ib/share/gromacs/top/aminoacids.dat

Re: [gmx-users] simulating two peptides in a box

2008-07-07 Thread kartik mehra 
Dear Justin,

1. They are the same protein ( 2 copies of the same protein)

2. The order in the .gro file seems fine... Basically it lists the
co-ordinates of a single copy of  peptide and then the solvent molecule ...
I presume since the .top file has 4 copies of the same molecule, this is how
the .gro file should look ?

3. Also is there an easier way of dealing with the modification of number of
solvent molecules ( since the co-ordinates involve a factor of 3 arising out
of the description of SPC atoms ... )





Thanks



>
> -
> From: Justin A. Lemkul <[EMAIL PROTECTED]>
> Date: Mon, Jul 7, 2008 at 11:30 AM
> Subject: Re: [gmx-users] simulating two peptides in a box
> To: Discussion list for GROMACS users 
>
>
>
>
> kartik mehra wrote:
>
>>
>>Dear Gromacs USers
>>
>>
>> 1. Please disregard the previous mail which was sent from a different
>> email id 
>>
>> 2. I have copied the relevant portion here ...( previous mail had a wrong
>> command ...I have copied the actual command here)
>>
>> Dear Justin,
>>
>>  Here is the exact error message : ( Here I have tried to simulate 4
>> protein molecules in a box ...basically I am looking at multiple molecule
>> interactions )
>>
>> *grompp  -f em.mdp -c nt17_sol.gro -o nt17_em.tpr -p nt17.top*
>>
>> *checking input for internal consistency...
>> calling /usr/bin/cpp...
>> processing topology...
>> Generated 279 of the 1225 non-bonded parameter combinations
>> Excluding 3 bonded neighbours for Protein 4
>> Excluding 2 bonded neighbours for SOL 8813
>> NOTE:
>>  System has non-zero total charge: 4.00e+00
>>
>> processing coordinates...
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (N - OW)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (H1 - HW1)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (H2 - HW2)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (H3 - OW)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (CG - OW)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (SD - HW1)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (CE - HW2)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
>> Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
>> (more than 20 non-matching atom names)
>> WARNING 1 [file "nt17.top", line 1126]:
>>  534 non-matching atom names
>>  atom names from nt17.top will be used
>>  atom names from nt17_sol.gro will be ignored
>>
>> double-checking input for internal consistency...
>> renumbering atomtypes...
>> converting bonded parameters...
>> #  BONDS:   17626
>> #   G96BONDS:   716
>> # ANGLES:   8813
>> #  G96ANGLES:   1040
>> #  PDIHS:   372
>> #  IDIHS:   320
>> #   LJ14:   1104
>> initialising group options...
>> processing index file...
>> Analysing residue names:
>> Opening library file
>> /usr/local/gromacs/3.3.1/64/gnu/ib/share/gromacs/top/aminoacids.dat
>> There are:  8813  OTHER residues
>> There are:68PROTEIN residues
>> There are: 0DNA residues
>> Analysing Protein...
>> Analysing Other...
>> Making dummy/rest group for T-Coupling containing 27151 elements
>> Making dummy/rest group for Acceleration containing 27151 elements
>> Making dummy/rest group for Freeze containing 27151 elements
>> Making dummy/rest group for Energy Mon. containing 27151 elements
>> Making dummy/rest group for VCM containing 27151 elements
>> Number of degrees of freedom in T-Coupling group rest is 81450.00
>> Making dummy/rest group for User1 containing 27151 elements
>> Making dummy/rest group for User2 containing 27151 elements
>> Making dummy/rest group for XTC containing 27151 elements
>> Making dummy/rest group for Or. Res. Fit containing 27151 elements
>> Making dummy/rest group for QMMM containing 27151 elements
>> T-Coupling   has 1 element(s): rest
>> Energy Mon.  has 1 element(s): rest
>> Acceleration has 1 element(s): rest
>> Freeze   has 1 element(s): rest
>> User1has 1 element(s): rest
>> User2has 1 element(s): rest
>> VCM  has 1 element(s): rest
>> XTC  has 1 elemen

Re: [gmx-users] simulating two peptides in a box

2008-07-07 Thread Rakesh Mishra 
Dear Justin,

 Here is the exact error message : ( Here I have tried to simulate 4 protein
molecules in a box ...basically I am looking at multiple molecule
interactions )

*grompp  -f em.mdp -c pep_sol.gro -o pep_em.tpr -p pep.top*

*checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 4
Excluding 2 bonded neighbours for SOL 8813
NOTE:
  System has non-zero total charge: 4.00e+00

processing coordinates...
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H1 - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H2 - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H3 - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CG - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (SD - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CE - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
(more than 20 non-matching atom names)
WARNING 1 [file "nt17.top", line 1126]:
  534 non-matching atom names
  atom names from nt17.top will be used
  atom names from nt17_sol.gro will be ignored

double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#  BONDS:   17626
#   G96BONDS:   716
# ANGLES:   8813
#  G96ANGLES:   1040
#  PDIHS:   372
#  IDIHS:   320
#   LJ14:   1104
initialising group options...
processing index file...
Analysing residue names:
Opening library file
/usr/local/gromacs/3.3.1/64/gnu/ib/share/gromacs/top/aminoacids.dat
There are:  8813  OTHER residues
There are:68PROTEIN residues
There are: 0DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 27151 elements
Making dummy/rest group for Acceleration containing 27151 elements
Making dummy/rest group for Freeze containing 27151 elements
Making dummy/rest group for Energy Mon. containing 27151 elements
Making dummy/rest group for VCM containing 27151 elements
Number of degrees of freedom in T-Coupling group rest is 81450.00
Making dummy/rest group for User1 containing 27151 elements
Making dummy/rest group for User2 containing 27151 elements
Making dummy/rest group for XTC containing 27151 elements
Making dummy/rest group for Or. Res. Fit containing 27151 elements
Making dummy/rest group for QMMM containing 27151 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.118 0.118 0.118
writing run input file...

Back Off! I just backed up nt17_em.tpr to ./#nt17_em.tpr.4#
There was 1 warning*

Any suggestions would be appreciated .. Also I do believe that the order
might be a problem..but isnt an inclusion of the no .of molecules meant to
take care of that ?

Thanks

Rakesh




On Mon, Jul 7, 2008 at 10:50 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

> Several questions come to mind, aside from trying to sift through your
> interpretation of error messages.  Hint: always show your exact command,
> followed by the relevant portion of the screen output; that way we don't
> have to guess what you've been up to :-)
>
> 1. Do you have two different proteins, or are they the same?  If they are
> different, changing the number of Protein molecules in your topology will
> not be correct.  If they are the same, this is fine.
>
> 2. Does the order of your topology follow the order of the coordinate file?
>  When you get warnings about non-matching atom names, you should be al

Re: [gmx-users] simulating two peptides in a box

2008-07-07 Thread Justin A. Lemkul 



kartik mehra wrote:


Dear Gromacs USers


1. Please disregard the previous mail which was sent from a different 
email id 


2. I have copied the relevant portion here ...( previous mail had a 
wrong command ...I have copied the actual command here)


Dear Justin,

 Here is the exact error message : ( Here I have tried to simulate 4 
protein molecules in a box ...basically I am looking at multiple 
molecule interactions )


*grompp  -f em.mdp -c nt17_sol.gro -o nt17_em.tpr -p nt17.top*

*checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 4
Excluding 2 bonded neighbours for SOL 8813
NOTE:
  System has non-zero total charge: 4.00e+00

processing coordinates...
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H1 - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H2 - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H3 - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CG - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (SD - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CE - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
(more than 20 non-matching atom names)
WARNING 1 [file "nt17.top", line 1126]:
  534 non-matching atom names
  atom names from nt17.top will be used
  atom names from nt17_sol.gro will be ignored

double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#  BONDS:   17626
#   G96BONDS:   716
# ANGLES:   8813
#  G96ANGLES:   1040
#  PDIHS:   372
#  IDIHS:   320
#   LJ14:   1104
initialising group options...
processing index file...
Analysing residue names:
Opening library file 
/usr/local/gromacs/3.3.1/64/gnu/ib/share/gromacs/top/aminoacids.dat

There are:  8813  OTHER residues
There are:68PROTEIN residues
There are: 0DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 27151 elements
Making dummy/rest group for Acceleration containing 27151 elements
Making dummy/rest group for Freeze containing 27151 elements
Making dummy/rest group for Energy Mon. containing 27151 elements
Making dummy/rest group for VCM containing 27151 elements
Number of degrees of freedom in T-Coupling group rest is 81450.00
Making dummy/rest group for User1 containing 27151 elements
Making dummy/rest group for User2 containing 27151 elements
Making dummy/rest group for XTC containing 27151 elements
Making dummy/rest group for Or. Res. Fit containing 27151 elements
Making dummy/rest group for QMMM containing 27151 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.118 0.118 0.118
writing run input file...

Back Off! I just backed up nt17_em.tpr to ./#nt17_em.tpr.4#
There was 1 warning*

Any suggestions would be appreciated .. Also I do believe that the 
order might be a problem..but isnt an inclusion of the no .of 
molecules meant to take care of that ?


Thanks 

 


OK, that's clear now.  What's happening is that grompp is finding water 
molecules where it should be finding protein.  Including a "number of 
protein molecules" does not automatically fix anything, necessarily.  
Again, I ask, are your proteins the same?


If they are different, you will need to have a mechanism something like:

#include "Protein_A.itp"
#include "Protein_B.itp"

#include "spc.itp"

#include "ions.itp"

to get the

Re: [gmx-users] simulating two peptides in a box

2008-07-07 Thread kartik mehra 
> Dear Gromacs USers


1. Please disregard the previous mail which was sent from a different email
id 

2. I have copied the relevant portion here ...( previous mail had a wrong
command ...I have copied the actual command here)

Dear Justin,

 Here is the exact error message : ( Here I have tried to simulate 4 protein
molecules in a box ...basically I am looking at multiple molecule
interactions )

*grompp  -f em.mdp -c nt17_sol.gro -o nt17_em.tpr -p nt17.top*

*checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 4
Excluding 2 bonded neighbours for SOL 8813
NOTE:
  System has non-zero total charge: 4.00e+00

processing coordinates...
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H1 - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H2 - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H3 - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CG - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (SD - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CE - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)
Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)
Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)
(more than 20 non-matching atom names)
WARNING 1 [file "nt17.top", line 1126]:
  534 non-matching atom names
  atom names from nt17.top will be used
  atom names from nt17_sol.gro will be ignored

double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#  BONDS:   17626
#   G96BONDS:   716
# ANGLES:   8813
#  G96ANGLES:   1040
#  PDIHS:   372
#  IDIHS:   320
#   LJ14:   1104
initialising group options...
processing index file...
Analysing residue names:
Opening library file
/usr/local/gromacs/3.3.1/64/gnu/ib/share/gromacs/top/aminoacids.dat
There are:  8813  OTHER residues
There are:68PROTEIN residues
There are: 0DNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for T-Coupling containing 27151 elements
Making dummy/rest group for Acceleration containing 27151 elements
Making dummy/rest group for Freeze containing 27151 elements
Making dummy/rest group for Energy Mon. containing 27151 elements
Making dummy/rest group for VCM containing 27151 elements
Number of degrees of freedom in T-Coupling group rest is 81450.00
Making dummy/rest group for User1 containing 27151 elements
Making dummy/rest group for User2 containing 27151 elements
Making dummy/rest group for XTC containing 27151 elements
Making dummy/rest group for Or. Res. Fit containing 27151 elements
Making dummy/rest group for QMMM containing 27151 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.118 0.118 0.118
writing run input file...

Back Off! I just backed up nt17_em.tpr to ./#nt17_em.tpr.4#
There was 1 warning*

Any suggestions would be appreciated .. Also I do believe that the order
might be a problem..but isnt an inclusion of the no .of molecules meant to
take care of that ?

Thanks



>
>
> -- Forwarded message --
> From: Justin A. Lemkul <[EMAIL PROTECTED]>
> Date: Mon, Jul 7, 2008 at 10:50 AM
> Subject: Re: [gmx-users] simulating two peptides in a box
> To: Discussion list for GROMACS users 
>
>
> Several questions come to mind, aside from trying to sift through your
> interpretation of error messages.  Hint: always show your exact command,
> followed by the relevant portion of the screen output; that way we don't
> have to guess what y

[gmx-users] Where is gmxtest gmxtest-3.3.3...

2008-07-07 Thread Kent F. Milfeld 
Hi,
  I've built and installed gromacs-3.3.3.  At the end of the install, it 
suggests that I "make tests".
  I do this, and find out that I need to install gmxtest.  At the Gromacs site, 
under downloads, I see only the gmxtest-3.3.2.tgz file (under the "Test Set" 
menu item).
  When I try using it, it becomes apparent(?) that the 3.3.2 tests are not set 
up to work with gromacs-3.3.3.  It fails with the error:

No topol.tpr file in angles1. grompp failed  (and others).

A search through the gmxtest-3.3.2 (directory and tar) shows no topol.tpr file.
Google shows a reference to gmxtest-3.3.3.tgz in the wiki.gromacs.org:

Test-set - wiki.gromacs.org
- 2 visits - 12:22pm
gmxtest-3.3.2.tgz * gmxtest-3.3.3.tgz. You can also get the test through the 
CVS interface. See the CVS_Howto for more information. Then: cvs co gmxtest ...


But I cannot get into the wiki.gromacs.org site.

1.) Is the wiki.gromacs.org site down, moved or removed?
2.) Does anybody know the link to gmxtest-3.3.3.tgz?

Would it be reasonable to include the test set with the gromacs distribution 
tar?  (I guess they are separated because of the large size for the tests, 8MB?)

Thanks,
Kent


Kent Milfeld
Texas Advanced Computing Center (TACC), 
www.tacc.utexas.edu
The University of Texas -- What Starts Here Changes The World
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Re: [gmx-users] simulating two peptides in a box

2008-07-07 Thread Justin A. Lemkul 
Several questions come to mind, aside from trying to sift through your 
interpretation of error messages.  Hint: always show your exact command, 
followed by the relevant portion of the screen output; that way we don't 
have to guess what you've been up to :-)


1. Do you have two different proteins, or are they the same?  If they 
are different, changing the number of Protein molecules in your topology 
will not be correct.  If they are the same, this is fine.


2. Does the order of your topology follow the order of the coordinate 
file?  When you get warnings about non-matching atom names, you should 
be alert that something has gone wrong.


-Justin

kartik mehra wrote:

Dear GMX Users,

I am trying to set up a simulation box with two proteins. I have 
perused the archives about the methodology of doing so. I tried the 
recommended option of changing the number of protein molecules in the 
topology file to 2. However when I run grompp after editconf and 
genbox, I get warning that the number of co -ordinates do not match 
(since I had not updated the number of solvent molecules ...) After 
updating the number of solvent molecules, when I try running grompp 
again, it shows a warning that the 23644 atom names do not match in 
top and gro files and that atom names from top files are being chosen .


Upon subsequent mdrun, the system explodes after a 1-4 interaction 
warning.


I was wondering whether anyone could help me out on this ... I do 
understand that the topic has been discussed pretty often but would 
appreciate any help ...



Cheers

Kartik

PS: I have not yet tried the other suggestion of translation and 
rotation followed by concatenating the two files





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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] simulating two peptides in a box

2008-07-07 Thread kartik mehra 
Dear GMX Users,

I am trying to set up a simulation box with two proteins. I have perused the
archives about the methodology of doing so. I tried the recommended option
of changing the number of protein molecules in the topology file to 2.
However when I run grompp after editconf and genbox, I get warning that the
number of co -ordinates do not match (since I had not updated the number of
solvent molecules ...) After updating the number of solvent molecules, when
I try running grompp again, it shows a warning that the 23644 atom names do
not match in top and gro files and that atom names from top files are being
chosen .

Upon subsequent mdrun, the system explodes after a 1-4 interaction warning.

I was wondering whether anyone could help me out on this ... I do understand
that the topic has been discussed pretty often but would appreciate any help
...


Cheers

Kartik

PS: I have not yet tried the other suggestion of translation and rotation
followed by concatenating the two files
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Re: [gmx-users] lipid itp file problem

2008-07-07 Thread Justin A. Lemkul 


It's difficult to tell what's going on.  You're using non-standard 
nomeclature for your atoms, so it's hard to tell where you got that 
structure file.  Typically, one sees DPPC start with C1, C2, C3, N4, 
etc. running sequentially with the normal numbering. 

Be aware that PRODRG is not changing atom *types* since this information 
is not in a coordinate file.  PRODRG has its own way of numbering and 
writing its output, so it is not terribly surprising that there are some 
differences.


It looks like there is something screwy with the input.pdb, though.  The 
oxygen atoms at the phosphate moiety show up disconnected in VMD, so the 
bonds are probably too long, and perhaps something is problematic 
there.  When I run your coordinates through PRODRG (to replicate the 
problem), PRODRG doesn't even generate a whole molecule, it finds two 
fragments!  So I don't know how you even succeeded in getting this 
output .gro file.


I'm assuming you already have a bilayer system from some source, since 
you had previously implanted a protein and whatever else.  Draw the 
molecule in PRODRG with the JME editor and see if it successfully runs.  
The atom nomenclature will be very different from standard numbering, 
but at least it will produce a complete topology.  Adjust the atom names 
to what they should be and try minimizing your structure again.


-Justin


serdar durdagi wrote:


Dear all,

 

I used beta version of PRODRG to produce G43a1 ff for a single DPPC 
molecule. When I try to make geometry optimisation, always I am facing 
with large Fmax values and large 1-4 interaction value.


 

When I visualize the *.gro file of the output, it seems some atom 
types are changed!


 


I am attaching input pdb file and output gro file.

 


What is the wrong thing here? Could any body tell me please?

 

 


Serdar

 


input pdb file:

 


TITLE Gyas ROwers Mature At Cryogenic Speed

REMARK THIS IS A SIMULATION BOX

CRYST1 45.149 45.149 45.149 90.00 90.00 90.00 P 1 1

MODEL 1

HETATM 1 N1 MOL 1 34.444 18.233 25.460 1.00 0.00

HETATM 2 C7 MOL 1 35.570 19.239 25.501 1.00 0.00

HETATM 3 C6 MOL 1 35.017 16.871 25.137 1.00 0.00

HETATM 4 C5 MOL 1 33.796 18.184 26.832 1.00 0.00

HETATM 5 C2 MOL 1 33.479 18.667 24.357 1.00 0.00

HETATM 6 C3 MOL 1 32.028 18.158 24.509 1.00 0.00

HETATM 7 O4 MOL 1 31.392 18.891 25.581 1.00 0.00

HETATM 8 P8 MOL 1 29.882 18.565 25.912 1.00 0.00

HETATM 9 O9 MOL 1 29.334 17.523 25.021 1.00 0.00

HETATM 10 O11 MOL 1 29.292 19.999 25.571 1.00 0.00

HETATM 11 C12 MOL 1 28.661 20.699 26.667 1.00 0.00

HETATM 12 C13 MOL 1 27.887 21.958 26.219 1.00 0.00

HETATM 13 O31 MOL 1 26.485 21.650 25.948 1.00 0.00

HETATM 14 C32 MOL 1 26.067 20.880 24.918 1.00 0.00

HETATM 15 O46 MOL 1 26.794 20.369 24.088 1.00 0.00

HETATM 16 C33 MOL 1 24.556 20.779 24.890 1.00 0.00

HETATM 17 C34 MOL 1 23.968 21.111 23.497 1.00 0.00

HETATM 18 C35 MOL 1 22.446 21.361 23.564 1.00 0.00

HETATM 19 C36 MOL 1 21.866 21.656 22.162 1.00 0.00

HETATM 20 C37 MOL 1 20.364 22.006 22.249 1.00 0.00

HETATM 21 C38 MOL 1 19.701 22.059 20.856 1.00 0.00

HETATM 22 C39 MOL 1 18.202 22.412 20.975 1.00 0.00

HETATM 23 C40 MOL 1 17.447 22.130 19.660 1.00 0.00

HETATM 24 C41 MOL 1 15.956 22.512 19.778 1.00 0.00

HETATM 25 C42 MOL 1 15.163 22.060 18.534 1.00 0.00

HETATM 26 C43 MOL 1 13.677 22.462 18.642 1.00 0.00

HETATM 27 C44 MOL 1 12.876 21.978 17.413 1.00 0.00

HETATM 28 C45 MOL 1 11.392 22.382 17.522 1.00 0.00

HETATM 29 C1 MOL 1 10.593 21.928 16.284 1.00 0.00

HETATM 30 C8 MOL 1 9.112 22.333 16.402 1.00 0.00

HETATM 31 C14 MOL 1 28.585 22.745 25.083 1.00 0.00

HETATM 32 O15 MOL 1 28.067 24.102 25.033 1.00 0.00

HETATM 33 C16 MOL 1 26.879 24.330 24.441 1.00 0.00

HETATM 34 O30 MOL 1 26.330 23.544 23.703 1.00 0.00

HETATM 35 C17 MOL 1 26.294 25.661 24.826 1.00 0.00

HETATM 36 C18 MOL 1 24.751 25.657 24.891 1.00 0.00

HETATM 37 C19 MOL 1 24.067 25.811 23.515 1.00 0.00

HETATM 38 C20 MOL 1 22.542 25.943 23.704 1.00 0.00

HETATM 39 C21 MOL 1 21.791 26.100 22.367 1.00 0.00

HETATM 40 C22 MOL 1 20.287 26.328 22.625 1.00 0.00

HETATM 41 C23 MOL 1 19.486 26.449 21.314 1.00 0.00

HETATM 42 C24 MOL 1 17.984 26.636 21.604 1.00 0.00

HETATM 43 C25 MOL 1 17.163 26.715 20.301 1.00 0.00

HETATM 44 C26 MOL 1 15.652 26.784 20.601 1.00 0.00

HETATM 45 C27 MOL 1 14.825 26.856 19.302 1.00 0.00

HETATM 46 C28 MOL 1 13.315 26.838 19.610 1.00 0.00

HETATM 47 C29 MOL 1 12.478 26.954 18.320 1.00 0.00

HETATM 48 C9 MOL 1 10.969 26.915 18.635 1.00 0.00

HETATM 49 C10 MOL 1 10.129 27.155 17.369 1.00 0.00

HETATM 50 O10 MOL 1 29.702 18.159 27.328 1.00 0.00

TER

ENDMDL

 

 


output pdb file

 

 


GROningen MAchine for Chemical Simulation in water

50

1MOL C31 1 3.445 1.823 2.546

1MOL C30 2 3.557 1.924 2.550

1MOL C29 3 3.502 1.687 2.514

1MOL C28 4 3.379 1.818 2.683

1MOL C27 5 3.347 1.867 2.435

1MOL C26 6 3.203 1.816 2.451

1MOL C25 7 3.139 1.889 2.558

1MOL C24 8 2.988 1.856 2.591

1MOL C23 9 2.933 1.752 2.502

1MOL C22 10 2.929 2.000 2.557

1MOL C21 11

[gmx-users] lipid itp file problem

2008-07-07 Thread serdar durdagi 





Dear all,
 
I used beta version of PRODRG to produce G43a1 ff for a single DPPC molecule. 
When I try to make geometry optimisation, always I am facing with large Fmax 
values and large 1-4 interaction value.
 
When I visualize the *.gro file of the output, it seems some atom types are 
changed!
 
I am attaching input pdb file and output gro file.
 
What is the wrong thing here? Could any body tell me please?
 
 
Serdar
 
input pdb file:
 
TITLE Gyas ROwers Mature At Cryogenic Speed
REMARK THIS IS A SIMULATION BOX
CRYST1 45.149 45.149 45.149 90.00 90.00 90.00 P 1 1
MODEL 1
HETATM 1 N1 MOL 1 34.444 18.233 25.460 1.00 0.00
HETATM 2 C7 MOL 1 35.570 19.239 25.501 1.00 0.00
HETATM 3 C6 MOL 1 35.017 16.871 25.137 1.00 0.00
HETATM 4 C5 MOL 1 33.796 18.184 26.832 1.00 0.00
HETATM 5 C2 MOL 1 33.479 18.667 24.357 1.00 0.00
HETATM 6 C3 MOL 1 32.028 18.158 24.509 1.00 0.00
HETATM 7 O4 MOL 1 31.392 18.891 25.581 1.00 0.00
HETATM 8 P8 MOL 1 29.882 18.565 25.912 1.00 0.00
HETATM 9 O9 MOL 1 29.334 17.523 25.021 1.00 0.00
HETATM 10 O11 MOL 1 29.292 19.999 25.571 1.00 0.00
HETATM 11 C12 MOL 1 28.661 20.699 26.667 1.00 0.00
HETATM 12 C13 MOL 1 27.887 21.958 26.219 1.00 0.00
HETATM 13 O31 MOL 1 26.485 21.650 25.948 1.00 0.00
HETATM 14 C32 MOL 1 26.067 20.880 24.918 1.00 0.00
HETATM 15 O46 MOL 1 26.794 20.369 24.088 1.00 0.00
HETATM 16 C33 MOL 1 24.556 20.779 24.890 1.00 0.00
HETATM 17 C34 MOL 1 23.968 21.111 23.497 1.00 0.00
HETATM 18 C35 MOL 1 22.446 21.361 23.564 1.00 0.00
HETATM 19 C36 MOL 1 21.866 21.656 22.162 1.00 0.00
HETATM 20 C37 MOL 1 20.364 22.006 22.249 1.00 0.00
HETATM 21 C38 MOL 1 19.701 22.059 20.856 1.00 0.00
HETATM 22 C39 MOL 1 18.202 22.412 20.975 1.00 0.00
HETATM 23 C40 MOL 1 17.447 22.130 19.660 1.00 0.00
HETATM 24 C41 MOL 1 15.956 22.512 19.778 1.00 0.00
HETATM 25 C42 MOL 1 15.163 22.060 18.534 1.00 0.00
HETATM 26 C43 MOL 1 13.677 22.462 18.642 1.00 0.00
HETATM 27 C44 MOL 1 12.876 21.978 17.413 1.00 0.00
HETATM 28 C45 MOL 1 11.392 22.382 17.522 1.00 0.00
HETATM 29 C1 MOL 1 10.593 21.928 16.284 1.00 0.00
HETATM 30 C8 MOL 1 9.112 22.333 16.402 1.00 0.00
HETATM 31 C14 MOL 1 28.585 22.745 25.083 1.00 0.00
HETATM 32 O15 MOL 1 28.067 24.102 25.033 1.00 0.00
HETATM 33 C16 MOL 1 26.879 24.330 24.441 1.00 0.00
HETATM 34 O30 MOL 1 26.330 23.544 23.703 1.00 0.00
HETATM 35 C17 MOL 1 26.294 25.661 24.826 1.00 0.00
HETATM 36 C18 MOL 1 24.751 25.657 24.891 1.00 0.00
HETATM 37 C19 MOL 1 24.067 25.811 23.515 1.00 0.00
HETATM 38 C20 MOL 1 22.542 25.943 23.704 1.00 0.00
HETATM 39 C21 MOL 1 21.791 26.100 22.367 1.00 0.00
HETATM 40 C22 MOL 1 20.287 26.328 22.625 1.00 0.00
HETATM 41 C23 MOL 1 19.486 26.449 21.314 1.00 0.00
HETATM 42 C24 MOL 1 17.984 26.636 21.604 1.00 0.00
HETATM 43 C25 MOL 1 17.163 26.715 20.301 1.00 0.00
HETATM 44 C26 MOL 1 15.652 26.784 20.601 1.00 0.00
HETATM 45 C27 MOL 1 14.825 26.856 19.302 1.00 0.00
HETATM 46 C28 MOL 1 13.315 26.838 19.610 1.00 0.00
HETATM 47 C29 MOL 1 12.478 26.954 18.320 1.00 0.00
HETATM 48 C9 MOL 1 10.969 26.915 18.635 1.00 0.00
HETATM 49 C10 MOL 1 10.129 27.155 17.369 1.00 0.00
HETATM 50 O10 MOL 1 29.702 18.159 27.328 1.00 0.00
TER
ENDMDL
 
 
output pdb file
 
 
GROningen MAchine for Chemical Simulation in water
50
1MOL C31 1 3.445 1.823 2.546
1MOL C30 2 3.557 1.924 2.550
1MOL C29 3 3.502 1.687 2.514
1MOL C28 4 3.379 1.818 2.683
1MOL C27 5 3.347 1.867 2.435
1MOL C26 6 3.203 1.816 2.451
1MOL C25 7 3.139 1.889 2.558
1MOL C24 8 2.988 1.856 2.591
1MOL C23 9 2.933 1.752 2.502
1MOL C22 10 2.929 2.000 2.557
1MOL C21 11 2.866 2.070 2.667
1MOL C20 12 2.788 2.195 2.622
1MOL C19 13 2.648 2.165 2.595
1MOL C18 14 2.607 2.088 2.492
1MOL C17 15 2.679 2.037 2.409
1MOL C15 16 2.456 2.078 2.489
1MOL O16 17 2.397 2.111 2.350
1MOL O14 18 2.245 2.136 2.356
1MOL C13 19 2.187 2.166 2.216
1MOL C12 20 2.036 2.201 2.225
1MOL O11 21 1.970 2.206 2.086
1MOL P8 22 1.820 2.241 2.097
1MOL O9 23 1.745 2.213 1.966
1MOL O10 24 1.596 2.251 1.978
1MOL O7 25 1.516 2.206 1.853
1MOL C6 26 1.368 2.246 1.864
1MOL C5 27 1.288 2.198 1.741
1MOL N4 28 1.139 2.238 1.752
1MOL C2 29 1.059 2.193 1.628
1MOL C3 30 0.911 2.233 1.640
1MOL C1 31 2.859 2.273 2.508
1MOL C32 32 2.806 2.412 2.503
1MOL O33 33 2.688 2.433 2.444
1MOL C34 34 2.633 2.354 2.370
1MOL O35 35 2.629 2.566 2.483
1MOL C36 36 2.475 2.566 2.489
1MOL C37 37 2.407 2.581 2.352
1MOL C38 38 2.254 2.594 2.370
1MOL C39 39 2.179 2.610 2.237
1MOL C40 40 2.029 2.633 2.262
1MOL C41 41 1.949 2.645 2.131
1MOL C42 42 1.798 2.664 2.160
1MOL C43 43 1.716 2.671 2.030
1MOL C44 44 1.565 2.678 2.060
1MOL C45 45 1.482 2.686 1.930
1MOL C46 46 1.332 2.684 1.961
1MOL C47 47 1.248 2.695 1.832
1MOL C48 48 1.097 2.692 1.864
1MOL C49 49 1.013 2.715 1.737
1MOL C50 50 2.970 1.816 2.733
4.51490 4.51490 4.51490
 
 
 
 
 
 
 


--- Justin A. Lemkul <[EMAIL PROTECTED]> schrieb am Mo, 7.7.2008:

Von: Justin A. Lemkul <[EMAIL PROTECTED]>
Betreff: Re: [gmx-users] lipid itp problem
An: [EMAIL PROTECTED], "Gromacs Users' List" 
Datum: Montag, 7. Juli 2008, 14:06

Please make sure to include the gmx-users

Re: [gmx-users] Re: Re: topology using prodrg (Diego Nolasco)

2008-07-07 Thread Diego Nolasco 
Take a look at John Kerrigan's tutorial?

http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf

And as said Justin, "There is no mention of Gromos87 in the topology line".

Diego.


2008/7/6 h a <[EMAIL PROTECTED]>:

> Yea I used the beta version and chose the force field GROMOS96.1. But after
> I run the server I get this output
>  Output example for the input thf.pdb
>
> *
> PRODRG> Starting up PRODRG version AA080107.0543
> PRODRG> Parameter set 'pd/gromos96' (fftype=2).
> PRODRG> PDB mode detected.
> PRODRG> WARNING: deleted hydrogen(s) from your input.
> PRODRG> Molecule complexity index: 2.00.
> PRODRG>   8 hydrogen(s) added.
> PRODRG> Using charge groups.
> PRODRG> Net charge on molecule:   0.000
> PRODRG>   9 partial charges  0 ambiguous
> PRODRG>  13 bonds0 ambiguous
> PRODRG>  25 bond angles  8 ambiguous
> PRODRG>   4 improper dihedrals   0 ambiguous
> PRODRG>   5 dihedrals0 ambiguous
> PRODRG> Writing GROMACS topology.
> PRODRG> GROMACS topology quality on 0-10 scale:  7.8
> GENDRG> Best structure was iteration 3211 with   3.20067739
> PRODRG> Spawning GROMACS version 3.3.3...
> PRODRG> RMSD from GROMOS bond ideality (Angstrom) :   0.003
> PRODRG> RMSD from GROMOS angle ideality (degrees) :   2.895
> PRODRG> RMSD from GROMOS plane ideality (degrees) :   5.553
> PRODRG> Number of improper improper dihedrals :   0
> PRODRG> RMSD from starting bonds (Angstrom)  :   0.011
> PRODRG> RMSD from starting angles (degrees)  :   0.464
> PRODRG> RMSD from starting planes (degrees)  :   0.000
> PRODRG> RMSD from starting coords (Angstrom) :   0.012
> PRODRG> Writing: SCRTHOWMMPG
> PRODRG> Normal program end.
>
>
>
>
> Click to go to the following output:
>
>   Coordinates
> # PDB (all H's [D][V], polar/aromatic H's [D][V], polar H's only [D][V] or
> no H's [D][V])
> # MDL Molfile (all H's [D][V], polar H's only [D][V] or no H's [D][V])
> # GROMOS87/GROMACS (all H's [D], polar/aromatic H's [D] or polar H's only
> [D])
> .
> .
> .
> .
> .
>
> The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens)
> .
> .
> .
> .
> .
> The GROMOS87/GROMACS coordinate file (all hydrogens)
> .
> .
> .
> The GROMACS topology
> .
> .
> .
> .
> .
> *
>
> It says that "parameter set 'pd/gromos96' " (in second line) but output was
> gromos87 coordinate files, topology files :( . can anybody explain why did
> this happen ? am I missing anything ?
>
> thank you,
>
> harshith
>
> >
> Are you sure you used prodrg beta?
>
> http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta
>
>
> 2008/7/4, h a <[EMAIL PROTECTED]>:
> >
> > Dear users,
> >
> > I am modeling polymer surface. I need topology for polystyrene. I used
> > prodrg earlier version and beta version but in both cases I get topology
> > for only GROMOS87 force field. Can not I get topology for force filed
> >
> > GROMOS96 ?
> >
> > also can anybody let me know what is .itp file for GOMOS87 force filed (
> I
> > mean similar to "GROMOS96 -> ffG43a1.itp" )
> >
> > thank you,
> >
> > Sincerely
> > ---
> > A.Harshith(Y6001)
> >
> > department of Bio Science and Bioengineering,
> > IIT Kanpur, India.
> > http://home.iitk.ac.in/~harshith  <
> http://home.iitk.ac.in/%7Eharshith>
> >
>
> ___
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[gmx-users] force constants of improper dihedrals in .itp file from prodrg

2008-07-07 Thread Joaquim Rui Rodrigues 
Dear all,

I am checking the itp file for my ligand obtained from prodrg beta, using 
gromos96.1 ff (43a1).  In the 
[ dihedrals ] section, I found lines such as 

; ai  aj  ak  al  fuc0, c1, m, ...
  31  32  24  28   2 35.3  334.8   35.3  334.8   ; impC4   N1   O1  
 C2   
  32  31  33  37   2  0.0  167.40.0  167.4   ; impN1   C4  C12  
C11   

for tetrahedral centres and substituents of rings, respectively,  that make 
sense, but also

  32  33  35  36   2  0.0  209.30.0  209.3   ; impN1  C12   N2  
C13  

for out-of-plane bending, for which I don't see where the force value (209.3) 
come from. From the 
ffG43a1bon.itp file, there are only 3 improper types:

#define gi_1   0.0   167.42309
; planar groups 40  
;
#define gi_2  35.26439   334.84617
; tetrahedral centres   80  
;
#define gi_3   0.0   669.69235
; heme iron 160 

Can someone explain how prodrg get the value for the force constant for 
out-of-plane bending of rings?
Also,  what is meaning of the (commented) values 40, 80 and 160 in this excerpt 
of ffG43a1bon.itp?

Many thanks,
Rui Rodrigues


--
Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)
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Re: [gmx-users] lipid itp problem

2008-07-07 Thread Justin A. Lemkul 


Please make sure to include the gmx-users list on correspondence; 
someone else may have a useful idea.


It looks to me that your "input.pdb" is badly broken.  Is this what 
PRODRG generated?  Are you using this structure for anything?  Where are 
the coordinates for your lipid bilayer coming from?


I would suggest starting over with the minimization - take the .pdb file 
that PRODRG generates (united-atom representation, as you've tried to 
use here), center it in a large box to avoid PBC effects (using editconf 
-c), and try again.


Just a general thought as well - it has long been said over this list 
that ffgmx should not be used for any new production simulations.  It is 
deprecated and the results from it may not be as reliable as one of the 
newer, Gromos96 force fields.  I would suggest using the PRODRG beta 
server to generate parameters under Gromos96 43a1.  None of this is 
likely the root cause of your problem, however.


-Justin

serdar durdagi wrote:


Hi Justin,

 


Thanks for your interest.

 

Yes, I tried your suggestion. But no success. I used a single DPPC 
molecule but I got same error message:


 


1-4 interaction is large.

 

When I checked, the gro file in VMD I didn't see the broken bonds 
but, very strange molecule. I attached the input pdb file and genrated 
gro file below, you can see how molecule seem now.


 


I used below top file and mdp file.

 


Thanks

 


Serdar

 

 

 


; File 'tat_last.top' was generated

; By user: durdagis (1004)

; On host: node25

; At date: Fri Dec 14 23:32:17 2007

;

; This is your topology file

; GROningen MAchine for Chemical Simulation

;

; Include forcefield parameters

#include "ffgmx.itp"

#include "lipid_july3.itp"

 

 


#ifdef FLEX_SPC

#include "flexspc.itp"

#else

#include "spc.itp"

#endif

 


; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

 


#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

GROningen MAchine for Chemical Simulation in water

[ molecules ]

; Compound #mols

MOL   1

 

 

 


title = vals

cpp = /usr/bin/cpp

define = -DFLEXIBLE

constraints = none

integrator = steep

dt = 0.002 ; ps !

nsteps = 500

nstlists = 10

ns_type = grid

rlist = 1.0

coulombtype = PME

rcoulomb = 1.0

vdwtype = cut-off

rvdw = 1.0

fourierspacing = 0.12

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

;

; Energy minimizing stuff

;

emtol = 100.0

emsteps = 0.01

 

 

 


input pdb file:

 


HETATM 3585 N1 MOL 344 94.416 32.830 63.679 1.00 0.00

HETATM 3586 C7 MOL 344 95.542 33.836 63.720 1.00 0.00

HETATM 3587 C6 MOL 344 94.989 31.468 63.356 1.00 0.00

HETATM 3588 C5 MOL 344 93.768 32.781 65.051 1.00 0.00

HETATM 3589 C2 MOL 344 93.451 33.264 62.576 1.00 0.00

HETATM 3590 C3 MOL 344 92.000 32.755 62.728 1.00 0.00

HETATM 3591 O4 MOL 344 91.364 33.488 63.800 1.00 0.00

HETATM 3592 P8 MOL 344 89.854 33.162 64.131 1.00 0.00

HETATM 3593 O9 MOL 344 89.306 32.120 63.240 1.00 0.00

HETATM 3594 O11 MOL 344 89.264 34.596 63.790 1.00 0.00

HETATM 3595 C12 MOL 344 88.633 35.296 64.886 1.00 0.00

HETATM 3596 C13 MOL 344 87.859 36.555 64.438 1.00 0.00

HETATM 3597 O31 MOL 344 86.457 36.247 64.167 1.00 0.00

HETATM 3598 C32 MOL 344 86.039 35.477 63.137 1.00 0.00

HETATM 3599 O46 MOL 344 86.766 34.966 62.307 1.00 0.00

HETATM 3600 C33 MOL 344 84.528 35.376 63.109 1.00 0.00

HETATM 3601 C34 MOL 344 83.940 35.708 61.716 1.00 0.00

HETATM 3602 C35 MOL 344 82.418 35.958 61.783 1.00 0.00

HETATM 3603 C36 MOL 344 81.838 36.253 60.381 1.00 0.00

HETATM 3604 C37 MOL 344 80.336 36.603 60.468 1.00 0.00

HETATM 3605 C38 MOL 344 79.673 36.656 59.075 1.00 0.00

HETATM 3606 C39 MOL 344 78.174 37.009 59.194 1.00 0.00

HETATM 3607 C40 MOL 344 77.419 36.727 57.879 1.00 0.00

HETATM 3608 C41 MOL 344 75.928 37.109 57.997 1.00 0.00

HETATM 3609 C42 MOL 344 75.135 36.657 56.753 1.00 0.00

HETATM 3610 C43 MOL 344 73.649 37.059 56.861 1.00 0.00

HETATM 3611 C44 MOL 344 72.848 36.575 55.632 1.00 0.00

HETATM 3612 C45 MOL 344 71.364 36.979 55.741 1.00 0.00

HETATM 3613 C1 MOL 344 70.565 36.525 54.503 1.00 0.00

HETATM 3614 C8 MOL 344 69.084 36.930 54.621 1.00 0.00

HETATM 3615 C14 MOL 344 88.557 37.342 63.302 1.00 0.00

HETATM 3616 O15 MOL 344 88.039 38.699 63.252 1.00 0.00

HETATM 3617 C16 MOL 344 86.851 38.927 62.660 1.00 0.00

HETATM 3618 O30 MOL 344 86.302 38.141 61.922 1.00 0.00

HETATM 3619 C17 MOL 344 86.266 40.258 63.045 1.00 0.00

HETATM 3620 C18 MOL 344 84.723 40.254 63.110 1.00 0.00

HETATM 3621 C19 MOL 344 84.039 40.408 61.734 1.00 0.00

HETATM 3622 C20 MOL 344 82.514 40.540 61.923 1.00 0.00

HETATM 3623 C21 MOL 344 81.763 40.697 60.586 1.00 0.00

HETATM 3624 C22 MOL 344 80.259 40.925 60.844 1.00 0.00

HETATM 3625 C23 MOL 344 79.458 41.046 59.533 1.00 0.00

HETATM 3626 C24 MOL 344 77.956 41.2

Re: [gmx-users] about some question on gromacs

2008-07-07 Thread Justin A. Lemkul 



anirban polley wrote:

Hi,
I have the following questions.
Are there any other ways to make bilayer other than packmol? I 
want to make bilayer (.pdb file).


Yes.  Read the genconf documentation; it should give you a reasonable 
start.  Also, have a thorough look through the list archives, this type 
of thing has been discussed before.


I saw that in GROMACS, there is united atom model, then what are 
the GROMACS computes in the Deuterium order parameter?


Not all lipid parameters are united-atom, but I'll assume that the ones 
you used are :-)  Think about basic molecular geometry.  Aren't all 
those carbon centers sp3 along the lipid chain?  Using some basic 
geometry, one can infer the hydrogen positions.


When I run the system for long time, the program suddenly crashes and 
says segmentation fault without giving any information for the 
reasons. Can you say what the probable reasons are for which the 
program crashes and says segmentation fault?


Absolutely not.  Without better information (screen output), there is no 
hope of diagnosing a segfault.  We have no idea what you're running, how 
you created it, how Gromacs was compiled (and which compilers), etc.  If 
you want free help, make it easy on us and tell us exactly what's going on.


-Justin


sincerely,
Anirban


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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] lipid itp problem

2008-07-07 Thread Justin A. Lemkul 
"Broken bonds" are probably a visualization artefact.  Did you try what 
I suggested about minimizing just DPPC?  Better yet, try minimizing one 
single DPPC molecule in vacuo to see if that succeeds, then move up to 
the bilayer, etc.


Also, increasing the table-extension is usually not going to solve 
anything.  If you're system is exploding, it's going to explode no 
matter what the table-extension is.


-Justin

serdar durdagi wrote:


Dear all,

 


Sorry for the previous e-mail format. I am writing again the problem.

 

I am trying to simulate drug at the binding site of the receptor 
surrounded by DPPC bilayer system. I have problem at the energy 
minimisation step. Always, I am getting below error message:


 

Warning: 1-4 interaction between 3642 and 3647 at distance 1.325 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, if 
not, you should increase table-extension in your mdp file


 

Step= 0, Dmax= 1.0e-02 nm, Epot= 7.16584e+15 Fmax= 5.29841e+18, atom= 
2662 Step= 1, Dmax= 1.0e-02 nm, Epot= 1.19114e+12 Fmax= 2.10320e+14, 
atom= 3605 Step= 2, Dmax= 1.2e-02 nm, Epot= 1.39843e+10 Fmax= 
8.84756e+11, atom= 2662 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.36040e+09 
Fmax= 5.31692e+10, atom= 2661


 

 

When I try to increase table-extension to more than 1.0, 1-4 
interaction always increases.


 

I checked the *.gro file, it seems during the minimisation, bonds at 
protein and drg molecules are fine however, bonds at the DPPC 
molecules are broken.


 

I guess problem is at the *.itp file of dppc. I produced *.itp file of 
DPPC from PRODRG. *itp file of lipid and *.mdp file for energy 
minimisation are attached below. Could any body give a clue for the 
solution? Many thanks in advanced.


 


Serdar Durdagi


 


;

;

; This file was generated by PRODRG version 071121.0636

; PRODRG written/copyrighted by Daan van Aalten

; and Alexander Schuettelkopf

;

; Questions/comments to [EMAIL PROTECTED]

;

; When using this software in a publication, cite:

; A. W. Schuettelkopf and D. M. F. van Aalten (2004).

; PRODRG - a tool for high-throughput crystallography

; of protein-ligand complexes.

; Acta Crystallogr. D60, 1355--1363.

;

;

[ moleculetype ]

; Name nrexcl

MOL 3

[ atoms ]

; nr type resnr resid atom cgnr charge mass

1 CH3 1 MOL C8 1 -0.033 15.0350

2 CH2 1 MOL C1 1 0.008 14.0270

3 CH2 1 MOL C45 1 0.008 14.0270

4 CH2 1 MOL C44 1 0.009 14.0270

5 CH2 1 MOL C43 1 0.008 14.0270

6 CH2 1 MOL C42 2 0.000 14.0270

7 CH2 1 MOL C41 2 0.000 14.0270

8 CH2 1 MOL C40 3 0.000 14.0270

9 CH2 1 MOL C39 3 0.000 14.0270

10 CH2 1 MOL C38 4 0.000 14.0270

11 CH2 1 MOL C37 4 0.000 14.0270

12 CH2 1 MOL C36 5 0.000 14.0270

13 CH2 1 MOL C35 5 0.000 14.0270

14 CH2 1 MOL C34 6 0.000 14.0270

15 CH2 1 MOL C33 7 0.036 14.0270

16 C 1 MOL C32 7 0.438 12.0110

17 O 1 MOL O46 7 -0.551 15.9994

18 OS 1 MOL O31 7 -0.160 15.9994

19 CS1 1 MOL C13 7 0.237 13.0190

20 CH2 1 MOL C12 8 0.000 14.0270

21 OS 1 MOL O11 9 -0.256 15.9994

22 P 1 MOL P8 9 0.998 30.9738

23 OM 1 MOL O10 9 -0.743 15.9994

24 OM 1 MOL O9 9 -0.743 15.9994

25 OS 1 MOL O4 9 -0.256 15.9994

26 CH2 1 MOL C3 10 0.041 14.0270

27 CH2 1 MOL C2 10 0.041 14.0270

28 NL 1 MOL N1 10 0.918 14.0067

29 CH3 1 MOL C6 11 0.000 15.0350

30 CH3 1 MOL C5 11 0.000 15.0350

31 CH3 1 MOL C7 12 0.000 15.0350

32 CS2 1 MOL C14 13 0.242 14.0270

33 OS 1 MOL O15 13 -0.162 15.9994

34 C 1 MOL C16 13 0.437 12.0110

35 O 1 MOL O30 13 -0.553 15.9994

36 CH2 1 MOL C17 13 0.036 14.0270

37 CH2 1 MOL C18 14 0.000 14.0270

38 CH2 1 MOL C19 14 0.000 14.0270

39 CH2 1 MOL C20 15 0.000 14.0270

40 CH2 1 MOL C21 15 0.000 14.0270

41 CH2 1 MOL C22 16 0.000 14.0270

42 CH2 1 MOL C23 16 0.000 14.0270

43 CH2 1 MOL C24 17 0.000 14.0270

44 CH2 1 MOL C25 17 0.000 14.0270

45 CH2 1 MOL C26 18 0.000 14.0270

46 CH2 1 MOL C27 19 0.008 14.0270

47 CH2 1 MOL C28 19 0.008 14.0270

48 CH2 1 MOL C29 19 0.008 14.0270

49 CH2 1 MOL C9 19 0.009 14.0270

50 CH3 1 MOL C10 19 -0.033 15.0350

[ bonds ]

; ai aj fu c0, c1, ...

1 2 1 0.153 334720.0 0.153 334720.0 ; C8 C1

2 3 1 0.153 334720.0 0.153 334720.0 ; C1 C45

3 4 1 0.153 334720.0 0.153 334720.0 ; C45 C44

4 5 1 0.153 334720.0 0.153 334720.0 ; C44 C43

5 6 1 0.153 334720.0 0.153 334720.0 ; C43 C42

6 7 1 0.153 334720.0 0.153 334720.0 ; C42 C41

7 8 1 0.153 334720.0 0.153 334720.0 ; C41 C40

8 9 1 0.153 334720.0 0.153 334720.0 ; C40 C39

9 10 1 0.153 334720.0 0.153 334720.0 ; C39 C38

10 11 1 0.153 334720.0 0.153 334720.0 ; C38 C37

11 12 1 0.153 334720.0 0.153 334720.0 ; C37 C36

12 13 1 0.153 334720.0 0.153 334720.0 ; C36 C35

13 14 1 0.153 334720.0 0.153 334720.0 ; C35 C34

14 15 1 0.153 334720.0 0.153 334720.0 ; C34 C33

15 16 1 0.153 334720.0 0.153 334720.0 ; C33 C32

16 17 1 0.123 502080.0 0.123 502080.0 ; C32 O46

16 18 1 0.136 376560.0 0.136 376560.0 ; C32 O31

18 19 1 0.144 251040.0 0.144 251040.0 ; O31 C13

19 20 1 0.153 251040.0 0.153 251040

[gmx-users] lipid itp problem

2008-07-07 Thread serdar durdagi 






Dear all,
 
Sorry for the previous e-mail format. I am writing again the problem.
 
I am trying to simulate drug at the binding site of the receptor surrounded by 
DPPC bilayer system. I have problem at the energy minimisation step. Always, I 
am getting below error message:
 
Warning: 1-4 interaction between 3642 and 3647 at distance 1.325 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, if not, you should 
increase table-extension in your mdp file
 
Step= 0, Dmax= 1.0e-02 nm, Epot= 7.16584e+15 Fmax= 5.29841e+18, atom= 2662 
Step= 1, Dmax= 1.0e-02 nm, Epot= 1.19114e+12 Fmax= 2.10320e+14, atom= 3605 
Step= 2, Dmax= 1.2e-02 nm, Epot= 1.39843e+10 Fmax= 8.84756e+11, atom= 2662 
Step= 3, Dmax= 1.4e-02 nm, Epot= 1.36040e+09 Fmax= 5.31692e+10, atom= 2661 
 
 
When I try to increase table-extension to more than 1.0, 1-4 interaction always 
increases.
 
I checked the *.gro file, it seems during the minimisation, bonds at protein 
and drg molecules are fine however, bonds at the DPPC molecules are broken. 
 
I guess problem is at the *.itp file of dppc. I produced *.itp file of DPPC 
from PRODRG. *itp file of lipid and *.mdp file for energy minimisation are 
attached below. Could any body give a clue for the solution? Many thanks in 
advanced. 
 
Serdar Durdagi 

 
; 
; 
; This file was generated by PRODRG version 071121.0636
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
; 
; Questions/comments to [EMAIL PROTECTED]
; 
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
; 
; 
[ moleculetype ]
; Name nrexcl
MOL 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 MOL C8 1 -0.033 15.0350 
2 CH2 1 MOL C1 1 0.008 14.0270 
3 CH2 1 MOL C45 1 0.008 14.0270 
4 CH2 1 MOL C44 1 0.009 14.0270 
5 CH2 1 MOL C43 1 0.008 14.0270 
6 CH2 1 MOL C42 2 0.000 14.0270 
7 CH2 1 MOL C41 2 0.000 14.0270 
8 CH2 1 MOL C40 3 0.000 14.0270 
9 CH2 1 MOL C39 3 0.000 14.0270 
10 CH2 1 MOL C38 4 0.000 14.0270 
11 CH2 1 MOL C37 4 0.000 14.0270 
12 CH2 1 MOL C36 5 0.000 14.0270 
13 CH2 1 MOL C35 5 0.000 14.0270 
14 CH2 1 MOL C34 6 0.000 14.0270 
15 CH2 1 MOL C33 7 0.036 14.0270 
16 C 1 MOL C32 7 0.438 12.0110 
17 O 1 MOL O46 7 -0.551 15.9994 
18 OS 1 MOL O31 7 -0.160 15.9994 
19 CS1 1 MOL C13 7 0.237 13.0190 
20 CH2 1 MOL C12 8 0.000 14.0270 
21 OS 1 MOL O11 9 -0.256 15.9994 
22 P 1 MOL P8 9 0.998 30.9738 
23 OM 1 MOL O10 9 -0.743 15.9994 
24 OM 1 MOL O9 9 -0.743 15.9994 
25 OS 1 MOL O4 9 -0.256 15.9994 
26 CH2 1 MOL C3 10 0.041 14.0270 
27 CH2 1 MOL C2 10 0.041 14.0270 
28 NL 1 MOL N1 10 0.918 14.0067 
29 CH3 1 MOL C6 11 0.000 15.0350 
30 CH3 1 MOL C5 11 0.000 15.0350 
31 CH3 1 MOL C7 12 0.000 15.0350 
32 CS2 1 MOL C14 13 0.242 14.0270 
33 OS 1 MOL O15 13 -0.162 15.9994 
34 C 1 MOL C16 13 0.437 12.0110 
35 O 1 MOL O30 13 -0.553 15.9994 
36 CH2 1 MOL C17 13 0.036 14.0270 
37 CH2 1 MOL C18 14 0.000 14.0270 
38 CH2 1 MOL C19 14 0.000 14.0270 
39 CH2 1 MOL C20 15 0.000 14.0270 
40 CH2 1 MOL C21 15 0.000 14.0270 
41 CH2 1 MOL C22 16 0.000 14.0270 
42 CH2 1 MOL C23 16 0.000 14.0270 
43 CH2 1 MOL C24 17 0.000 14.0270 
44 CH2 1 MOL C25 17 0.000 14.0270 
45 CH2 1 MOL C26 18 0.000 14.0270 
46 CH2 1 MOL C27 19 0.008 14.0270 
47 CH2 1 MOL C28 19 0.008 14.0270 
48 CH2 1 MOL C29 19 0.008 14.0270 
49 CH2 1 MOL C9 19 0.009 14.0270 
50 CH3 1 MOL C10 19 -0.033 15.0350 
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; C8 C1 
2 3 1 0.153 334720.0 0.153 334720.0 ; C1 C45 
3 4 1 0.153 334720.0 0.153 334720.0 ; C45 C44 
4 5 1 0.153 334720.0 0.153 334720.0 ; C44 C43 
5 6 1 0.153 334720.0 0.153 334720.0 ; C43 C42 
6 7 1 0.153 334720.0 0.153 334720.0 ; C42 C41 
7 8 1 0.153 334720.0 0.153 334720.0 ; C41 C40 
8 9 1 0.153 334720.0 0.153 334720.0 ; C40 C39 
9 10 1 0.153 334720.0 0.153 334720.0 ; C39 C38 
10 11 1 0.153 334720.0 0.153 334720.0 ; C38 C37 
11 12 1 0.153 334720.0 0.153 334720.0 ; C37 C36 
12 13 1 0.153 334720.0 0.153 334720.0 ; C36 C35 
13 14 1 0.153 334720.0 0.153 334720.0 ; C35 C34 
14 15 1 0.153 334720.0 0.153 334720.0 ; C34 C33 
15 16 1 0.153 334720.0 0.153 334720.0 ; C33 C32 
16 17 1 0.123 502080.0 0.123 502080.0 ; C32 O46 
16 18 1 0.136 376560.0 0.136 376560.0 ; C32 O31 
18 19 1 0.144 251040.0 0.144 251040.0 ; O31 C13 
19 20 1 0.153 251040.0 0.153 251040.0 ; C13 C12 
19 32 1 0.152 251040.0 0.152 251040.0 ; C13 C14 
20 21 1 0.143 251040.0 0.143 251040.0 ; C12 O11 
21 22 1 0.161 251040.0 0.161 251040.0 ; O11 P8 
22 23 1 0.148 376560.0 0.148 376560.0 ; P8 O10 
22 24 1 0.148 376560.0 0.148 376560.0 ; P8 O9 
22 25 1 0.161 251040.0 0.161 251040.0 ; P8 O4 
25 26 1 0.143 251040.0 0.143 251040.0 ; O4 C3 
26 27 1 0.153 334720.0 0.153 334720.0 ; C3 C2 
27 28 1 0.147 376560.0 0.147 376560.0 ; C2 N1 
28 29 1 0.147 376560.0 0.147 376560.0

RE: [gmx-users] about deuterium order parameter

2008-07-07 Thread Kukol, Andreas 
Dear Anirban,

In order to answer your first question about sn1/sn2 chain, you should do some 
background reading about the molecular structure of phospholipids and look at 
some experimental or simulation papers, where order parameters have been 
reported.

In order to make the index file, you first delete all groups: del 0-4

Then you create one group fore EACH carbon atom in the chain:
a C13
a C14
a C15
... and so on

Do the same for the other tail as a separate index file. The atom names in each 
tail should be different and not start both at C13.

Best wishes
Andreas


>>
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of anirban polley
Sent: 07 July 2008 05:25
To: gmx-users@gromacs.org
Subject: [gmx-users] about deuterium order parameter

Hello,
   I want to analyze the deuterium order parameter of a system contains 
DPPC, sphingomyelin(SM) and cholesterol(CHOL) and water(SOL). I read from the 
prevous mail that I have to make index file for sn1 and sn2.
Now, my first question  is what the meaning of sn1 and sn2 is. How can I assign 
from the .pdb file of the total system.
 make_ndx -f dppc20-sm20-cholesterol20-water200tolerance3-bilayer50x50x54.pdb
  0 System  :  3180 atoms
  1 DPP :  1000 atoms
  2 SM  :  1000 atoms
  3 CHOL:   580 atoms
  4 SOL :   600 atoms

 nr : group   !   'name' nr name   'splitch' nrEnter: list groups
 'a': atom&   'del' nr 'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr'splitat' nr'h': help
 'r': residue 'res' nr 'chain' char
 "name": group'case': case sensitive   'q': save and quit
   I understand that after giving the make_ndx command, I have to use above 
of these command ( a, t r ). But what are the full command so that I can make 
clear nice index file for the analysis of deuterium order parameter.
  In my case, for the the numbering of DPPC is like that : two tail starts 
from C13 to C31 and C13 to C50;
SM is like 
that: two tails starts from C13 to C32 and C13 to C50;
CHOL is like that : 
OH group is at 6 & 7and small tail comes from C21 to C29.
Can you write the full command so that I can clearly understand clearly.
Because, the next step I know that is
g_order -f name.trr -n index.ndx -s topol.tpr -od

Please, can you give the answer for me ?
 Sincerely,
Anirban



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[gmx-users] about some question on gromacs

2008-07-07 Thread anirban polley 
Hi,
I have the following questions.
Are there any other ways to make bilayer other than packmol? I want to
make bilayer (.pdb file).
I saw that in GROMACS, there is united atom model, then what are the
GROMACS computes in the Deuterium order parameter?
When I run the system for long time, the program suddenly crashes and says
segmentation fault without giving any information for the reasons. Can you
say what the probable reasons are for which the program crashes and says
segmentation fault?
sincerely,
Anirban
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