date:20081107


Bhawana Gupta wrote:

hello everyone,
 
pls tell me that whether we can use gromacs for simulating pdb with 3 or 
4 residue.


Yes. You can use GROMACS to simulate traffic if you want to. :-)

As i had done it with 4 residue with blocking group. But then i got the 
error for rvdw and rlist as they should be nearer to cutoff value.
So instead of decreasing the value of rvdw. i increased my X, Y, Z 
coordinates.

Tell me whether i m correct or not.


We can't possibly tell because we don't know
a) your objective and
b) what sizes you've tried, and
c) what force field you're trying to use, and
d) what errors you've received and
e) what other problems you've encountered.
f) how you've tried to solve the above.

Please read the contents of http://wiki.gromacs.org/index.php/Support 
and consider how you can better use the resources of people who might be 
prepared to help you. Remember, it's not our job to do so, and 
frustrated though you might be, you need to work hard to interact 
successfully with the mailing list too.


rcoulomb and rvdw should stay close to the values used for 
parameterizing that force field. If you don't know what they are, go and 
read up.



One more thing
whether we can apply position restraint to all the atoms in the 
file.whether it will have any impact on my output.

Silly Ouestion. But sorry for that.


Yes you can. But then you will have dynamics subject to position 
restraints. That's not usually a useful thing.


How we can come to know that to which atom i add position restraint in 
posre.itp file.Sorry i don't Know about this

I read the manual but i m confused.


The format of the [ position_restraints ] section is explained in 
chapter 5. There's an example there. The underlying maths is in chapter 
4. It's really not that hard.


Have you done all of the tutorial material you can find? This will teach 
you some of the normal ways of doing things. It's much easier to make up 
your protocol to suit your objectives once you've seen a range of things 
work.


Mark
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[gmx-users] position restraint and pdb

hello everyone,

pls tell me that whether we can use gromacs for simulating pdb with 3 or 4
residue.
As i had done it with 4 residue with blocking group. But then i got the
error for rvdw and rlist as they should be nearer to cutoff value.
So instead of decreasing the value of rvdw. i increased my X, Y, Z
coordinates.
Tell me whether i m correct or not.

One more thing
whether we can apply position restraint to all the atoms in the file.whether
it will have any impact on my output.
Silly Ouestion. But sorry for that.
How we can come to know that to which atom i add position restraint in
posre.itp file.Sorry i don't Know about this
I read the manual but i m confused.

Pls help me out

Bhawana
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Re: [gmx-users] Re: High frequency output slow down the simulation?


xianghong qi wrote:

Hello, all:
 
I compare the two simulations with different output frequency for .xtc 
file in same machine. One with low frequency runs  much faster than the 
one with high frequency. 
Is that reasonable? I think the frequency shouldn't affect the 
simulation speed.  
 
Anyone has idea about this situation?  Thanks.  


If that's really the only difference between the two simulations, then 
it suggests your file system has severe problems. With modern buffered 
I/O it's inconceivable that writing output could rate-limit GROMACS. 
(Unless something's broken in 4.x, but you haven't said what you're using.)


Mark
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[gmx-users] Re: High frequency output slow down the simulation?

2008-11-07 Thread xianghong qi

Hello, all:

I compare the two simulations with different output frequency for .xtc file
in same machine. One with low frequency runs  much faster than the one with
high frequency.
Is that reasonable? I think the frequency shouldn't affect the simulation
speed.

Anyone has idea about this situation?  Thanks.
-Xianghong Qi

-- 
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Re: [gmx-users] g_rms


Tatsiana Kirys wrote:

Hi,

i got strange results using g_rms.
Does it by default uses mass weighting for superposition? 
I wrote my own script to calculate rmsd without mass weighting and it gives different results then using g_rms. 
If it uses mass weighting for superposition how not not use it? i tried select "-mw no", but it doesn't work.


As always, g_rms -h explains some relevant issues here.

Also, "it doesn't work" is also a useless description for helping us 
help you. :-)


Mark
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[gmx-users] g_rms

2008-11-07 Thread Tatsiana Kirys


Hi,

i got strange results using g_rms.
Does it by default uses mass weighting for superposition? 
I wrote my own script to calculate rmsd without mass weighting and it gives 
different results then using g_rms. 
If it uses mass weighting for superposition how not not use it? i tried select 
"-mw no", but it doesn't work.


namy thanks
Tania
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Re: [gmx-users] Simulation of difloromethane

Polavarapu, Abhigna wrote:

Hi all,
I am just running a test simulation for normal modes. I am unable to create a topology file for diflormethane
as gromacs say "unrecognized MOL residue type". I created it manually but now it says " Invalid order
for directive moleculetype, file ""topol.top"", line 17". Please tell me how to convert a
molecule file with MOL types to gromacs topology and cordinate files.

Something in your topology is out of order ("invalid order for directive..." is
indicative of that problem). Search the archives for similar messages and read
Chapter 5 of the manual thoroughly.

If you need further help, it is nearly impossible to diagnose such a problem
unless you actually post it to the list.

-Justin

Thank you
abhigna
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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] Simulation of difloromethane

2008-11-07 Thread Polavarapu, Abhigna

Hi all,
  I am just running a test simulation for normal modes. I am unable to 
create a topology file for diflormethane as gromacs say "unrecognized MOL 
residue type". I created it manually but now it says " Invalid order for 
directive moleculetype, file ""topol.top"", line 17". Please tell me how to 
convert a molecule file with MOL types to gromacs topology and cordinate files.

Thank you
abhigna
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Re: [gmx-users] Water model => amber port to gromacs




Chih-Ying Lin wrote:

HI
Here are the links.
 Water model => amber port to gromacs

http://www.gromacs.org/pipermail/gmx-users/2007-June/027817.html

http://www.gromacs.org/pipermail/gmx-users/2007-June/027823.html

http://www.gromacs.org/pipermail/gmx-users/2007-June/027840.html


 The two steps are shown on the above links.
 1. #include ffamber_tip*pin the .top file
 2. include an #ifdef_FF_AMBER statement in tip*p.itp

Should I also #include ffamber99.itp in the .top file?




You always have to call the force field at the beginning of your .top, or else 
grompp will not know which parameters to apply to the atoms in your system.  I 
would suggest a thorough read of Chapter 5 in the manual for how all of this works.


-Justin


Thank you
Lin






Chih-Ying Lin wrote:

Hi
Water model => amber port to gromacs

The two steps are shown on the archive.
1. #include ffamber_tip*pin the .top file
2. include an #ifdef_FF_AMBER statement in tip*p.itp


If you want others' opinions for free, please provide links - and test
them first to see that you've linked to the content, and not some
wrapper page/frame! :-)


Should I also #include ffamber99.tip in the .top file?


"tip" does not equal "itp" :-)

Mark
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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] Water model => amber port to gromacs

2008-11-07 Thread Chih-Ying Lin

HI
Here are the links.
 Water model => amber port to gromacs

http://www.gromacs.org/pipermail/gmx-users/2007-June/027817.html

http://www.gromacs.org/pipermail/gmx-users/2007-June/027823.html

http://www.gromacs.org/pipermail/gmx-users/2007-June/027840.html

 The two steps are shown on the above links.
 1. #include ffamber_tip*pin the .top file
 2. include an #ifdef_FF_AMBER statement in tip*p.itp

Should I also #include ffamber99.itp in the .top file?

Thank you
Lin

Chih-Ying Lin wrote:
> Hi
> Water model => amber port to gromacs
>
> The two steps are shown on the archive.
> 1. #include ffamber_tip*pin the .top file
> 2. include an #ifdef_FF_AMBER statement in tip*p.itp

If you want others' opinions for free, please provide links - and test
them first to see that you've linked to the content, and not some
wrapper page/frame! :-)

> Should I also #include ffamber99.tip in the .top file?

"tip" does not equal "itp" :-)

Mark
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Re: [gmx-users] Re: .xtc file is incomplete

2008-11-07 Thread xianghong qi

Thanks so much, Chris. I will check wiki.
-Xianghong Qi

On Fri, Nov 7, 2008 at 10:44 AM, <[EMAIL PROTECTED]> wrote:

> We have experienced this with NFS delay problems if you try to access the
> fie before it is completely written. On our most frustrating server, it can
> take up to an hour for the .xtc to be written in rare cases. For us, the
> biggest problem is when the .trr and .edr are completely written but the
> .xtc is not. Therefore one may not notice for many days and end up unable to
> make a nice movie to show your colleagues. To combat this, I developed an
> automated checkpointing script that you can find in the
> beginners->checkpointing jobs section of the gromacs wiki.
>
> Chris.
>
>
> xianghong qi wrote:
>>
>>Hello, everyone:
>>
>>when I run simulation, I got incomplete .xtc file, incomplete
>>.trr file, but I have a complete log file. Then I use this
>>incomplete to create input file for mdrun, I got the reasonable
>>size of .tpr file.
>>
>>
>>I wouldn't trust that .tpr file to contain what you think it does
>>(size doesn't matter), at least in terms of the starting time.  It
>>will take the last frame as input, whatever it may be in the .trr file.
>>
>>
>>I am confused what happed there. Does anyone has some idea about
>>this?
>>
>>
>>Probably a hardware blip caused the last frame(s) to not be written.
>> I've had that happen before.
>>
>>
>>actually, when I rerun my simulation, I got the complete .xtc
>>file . I don't know why.
>>
>>
>>Probably because the blip didn't happen again :)
>>
>>-Justin
>>
>
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Re: [gmx-users] freeze group gives Segmentation fault


[EMAIL PROTECTED] wrote:

Hi!

I am trying to use freezegroups on an ice-crystal. grompp gives no warning.
Trying the same simulation but removing the freezegroup works.


We're not mind-readers :-) Why do you think it's not working? What do 
you see on stdout? In the various output files?



Please note my mdp-file's attached


That's a start. It's a bit like taking one's car to the mechanic. The 
fact that you brought it in means you think something's probably wrong, 
but it'll cost you a lot more or take lots more time if you don't tell 
them things you've found out.


Mark
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Re: [gmx-users] mdp file


He, Yang wrote:

Hi Mark,

This is what I got when I use the command gmxcheck:

Checking file traj.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  34
Last frame  1 time0.100


Item#frames Timestep (ps)
Step 20.1
Time 20.1
Lambda   20.1
Coords   20.1
Velocities   20.1
Forces   0
Box  20.1

Also, I have tried to increase  the value of nsteps to 1, but no change 
happened still just the static figure.

I really got stuck about that.

Hope to get your further suggestions,


I think what I said last time covers it pretty well. You're crashing and 
I gave you a link to somewhere with some explanations and ideas. Fix that.


Mark
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[gmx-users] freeze group gives Segmentation fault

2008-11-07 Thread ilona . baldus


Hi!

I am trying to use freezegroups on an ice-crystal. grompp gives no warning.
Trying the same simulation but removing the freezegroup works.

Please note my mdp-file's attached

Ilona


;
;   File 'mdout.mdp' was generated
;   By user: bq_ibaldus (2417)
;   On host: cln-fg06
;   At date: Fri Nov  7 15:53:11 2008
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  = 
; e.g.: -DI_Want_Cookies -DMe_Too
define   = 

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 500
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm-mode= none
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps= 

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 0.01
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 100
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 1
nstvout  = 1
nstfout  = 1
; Output frequency for energies to log file and energy file
nstlog   = 1
nstenergy= 500
; Output frequency and precision for xtc file
nstxtcout= 1000
xtc_precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = 
; Selection of energy groups
energygrps   = crystal

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.5

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = cut-off
rcoulomb_switch  = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths   
rvdw_switch  = 0
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  = 
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent   = 80
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension   = 2.092

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl   = Berendsen
; Groups to couple separately
tc_grps  = crystal
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t

[gmx-users] Re: .xtc file is incomplete

2008-11-07 Thread chris . neale

We have experienced this with NFS delay problems if you try to access  
the fie before it is completely written. On our most frustrating  
server, it can take up to an hour for the .xtc to be written in rare  
cases. For us, the biggest problem is when the .trr and .edr are  
completely written but the .xtc is not. Therefore one may not notice  
for many days and end up unable to make a nice movie to show your  
colleagues. To combat this, I developed an automated checkpointing  
script that you can find in the beginners->checkpointing jobs section  
of the gromacs wiki.


Chris.



xianghong qi wrote:

Hello, everyone:

when I run simulation, I got incomplete .xtc file, incomplete
.trr file, but I have a complete log file. Then I use this
incomplete to create input file for mdrun, I got the reasonable
size of .tpr file.


I wouldn't trust that .tpr file to contain what you think it does
(size doesn't matter), at least in terms of the starting time.  It
will take the last frame as input, whatever it may be in the .trr file.


I am confused what happed there. Does anyone has some idea about
this?


Probably a hardware blip caused the last frame(s) to not be written.
 I've had that happen before.


actually, when I rerun my simulation, I got the complete .xtc
file . I don't know why.


Probably because the blip didn't happen again :)

-Justin


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[gmx-users] Spatial distribution

2008-11-07 Thread chris . neale

I wrote g_spatial and it should produce a spatial distribution  
function. However, it's rather complicated to use. Did you follow the  
directions in g_spatial -h ? There are about 10 steps to use it. It is  
so complicated on purpose in order to give the user full flexibility,  
but this means that you need to do all of your alignment yourself. If  
you did that correctly, then I also suggest that you should make sure  
that you are visualizing it correctly in VMD. By default you will see  
some atoms, but that is only there because VMD will not recognize a  
gaussian cube without any atoms, and also it makes it easier for you  
to ensure that any other pdbs you may load overlay correctly.  
Therefore ensure that you switch the representation to isosurface and  
then slide the bar so that you see the appropriate isosurface contour.


Please report back to the list with findings so that other users can  
later benifit from your work


Chris.

Gadzikano Munyuki wrote:
I want to analyse the solvent around a peptide . I used g_sdf and  
the output  that i am getting (i.e the refmol.gro) does not have the  
whole peptide molecule but just the residues that i use to define  
the coordinate system . I then tried to use g_spatialbut its doing  
something very different and not spatial distibution, it looks like   
its executing g_cluster instead. I was wondering if g_custer and  
g_spatial are meant to do the same thing.


Have a read of g_cluster -h and g_spatial -h and decide whether they're
doing the same thing :-)

Mark

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Re: Re: [gmx-users] rmsd on homologous protein structure

2008-11-07 Thread Tatsiana Kirys

tahnk you i'll try that

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RE: [gmx-users] mdp file

2008-11-07 Thread He, Yang

Hi Mark,

This is what I got when I use the command gmxcheck:

Checking file traj.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  34
Last frame  1 time0.100

Item#frames Timestep (ps)
Step 20.1
Time 20.1
Lambda   20.1
Coords   20.1
Velocities   20.1
Forces   0
Box  20.1

Also, I have tried to increase  the value of nsteps to 1, but no change 
happened still just the static figure.

I really got stuck about that.

Hope to get your further suggestions,

Thank you .

Yang

From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL 
PROTECTED]
Sent: Thursday, November 06, 2008 3:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdp file

He, Yang wrote:
> Hi all users,
>
> When I use the command "mdrun -tablep table.xvg " to run my model in gromacs, 
>  it always shows that:
>
> starting mdrun 'DNA in water'
> 1 steps, 20.0 ps.

This is orders of magnitude too short to expect a large conformational
change to happen. Think nanoseconds at least. Depending on the number of
base pairs, think much more than that. You should be aware of how long
this might take, since you've read some literature about MD on DNA, right?

> Warning: 1-4 interaction between 11 and 19 at distance 1.437 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

Don't ignore warnings unless you know what they mean and it's OK. See
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off

> And no more information . Furthermore, I use the command ngmx to look at the 
> trajectory , I found that  only when I set the value of nsteps by 10,  will 
> there be little animation about my DNA two strands' disassociation . While I 
> try to reduce the value of dt , nstdisreout , nstorireout and nstdihreout , 
> it also did not work and I can not see any disassociation of DNA strands  
> using the command "ngmx".

Probably, you only wrote one frame before it crashed. Does the log file
look like it terminated normally after 1 steps? Use gmxcheck to see
how many frames you have in the trajectory file.

> Also, what I got confused is that when I set the value of nsteps larger than 
> 10, there is just static figure about DNA model.  This is my part of mdp file

1) You need the simulation not to crash
2) You need to simulate for long enough (nsteps) to see a change
3) You need to write output (nstxout or nstxtcout) sufficiently often to
keep yourself happy.

Mark
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[gmx-users] MD run, polarizable molecules, EM did not converge

2008-11-07 Thread Andreas Kring


Hello all.

I've been searching the archives with no luck so here goes:

I am using shell molecular dynamics to simulate a hydroxide ion 
dissolved in water. I have been using the steepest descent minimizer 
(tried in the range from 30 to 70 steps) to minimize the system, 
but I'm not capable of getting Fmax lower than


Potential Energy  = -2.39282728357508e+04
Maximum force =  2.22634509434073e+03 on atom 3
Norm of force =  5.74522076456533e+01

Running the shell MD simulation with the output from the above 
minimization generates a lot of "EM did not converge" (see below). As 
recommended in the GROMACS manual, I'm using the follow parameters in 
the mdp-file:


emtol = 1
niter = 20
fcstep = 0

step 1: EM did not converge in 20 iterations, RMS force 307.457
step 2: EM did not converge in 20 iterations, RMS force 306.841
step 3: EM did not converge in 20 iterations, RMS force 308.809
...

Any ideas on how I can fix this?

Regards
Andreas
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Re: [gmx-users] missing of methyl at N-terminal


Bhawana Gupta wrote:

thankyou for ur reply.
exact error which i m getting, when running pdb2gmx command with the pdb 
which i had taken from insightII is

Program pdb2gmx, VERSION 4.0
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C in residue NH2 6 not found in rtp entry with 3 atoms
 while sorting atoms


So from this you can work out that pdb2gmx is guessing that residue 6 
(named "NHM" in your pdb file) is intended to be an NH2 residue (which 
has 3 atoms), but then gets confused trying to match one of them to the 
C atom in the residue named "NHM". You need to name residues according 
to the names in the .rtp database. Here, "NHM" presumably isn't right 
for N-methylamine your force field. Go and look up what it should be and 
edit your input to help pdb2gmx along.


Computers can't be programmed to guess correctly in all cases what the 
user meant. You need to take some responsibility for telling it useful 
things :-) A good working knowledge of the contents of chapter 5 of the 
manual is invaluable here.


Mark
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Re: [gmx-users] Spatial distribution


Gadzikano Munyuki wrote:

I want to analyse the solvent around a peptide . I used g_sdf and the output  
that i am getting (i.e the refmol.gro) does not have the whole peptide molecule 
but just the residues that i use to define the coordinate system . I then tried 
to use g_spatialbut its doing something very different and not spatial 
distibution, it looks like  its executing g_cluster instead. I was wondering if 
g_custer and g_spatial are meant to do the same thing.


Have a read of g_cluster -h and g_spatial -h and decide whether they're 
doing the same thing :-)


Mark
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Re: [gmx-users] Misunderstandings with g_rms


Jochen Hub wrote:

DimitryASuplatov wrote:

Hello,

I am sorry for this stupid question.

Lets say I have an index file of all chain A atoms. I want to calculate
RMS of chain A _backbone_ only.

I run g_rms. It asks two questions:
1/ Select group for least squares fit
2/ Select group for RMSD calculation

To the best of my understanding, I should answer "BACKBONE" to the first
question and enter group number corresponding to chain A index file to
the second one.


In your case you need to make an index file with a group of the backbone
of chain a, do something like

make_ndx -f x.gro
chain a
"ChA" & Backbone
q

then run g_rms with -n

And give the ChainA-backbone group twice to g_rms.


It's not necessarily true that the group used for fitting should be the 
group for the RMSD calculation - that's why g_rms allows them to be 
different. People should consider their objective and choose 
appropriately in each case.


Mark
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Re: [gmx-users] Running MDS over docked poses




vivek sharma wrote:

Hi Andreas,
 Thanks for your response.
But I am not finding option for AMBER forcefield in gromacs (during 
pdb2gmx step). which of the 9 force-field I should use for the same.




You have to download and install the ffamber ports:

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

-Justin



With Thanks,
Vivek

2008/11/7 Kukol, Andreas <[EMAIL PROTECTED] >

Hi,

Autodock4 uses the AMBER forcefield, so that would be a good
starting point for gromacs as well.

In order to set the temperature for a particular group
1) you generate an index file containing all the atoms in your GROUP
2) in your mdp-file specify GROUP as a separate temperature coupling
group and specify the temperature you want
3) use grompp with -n yourindexfile.ndx

Note sure, if this is makes physically sense though.

Andreas


 >
From: [EMAIL PROTECTED]

[mailto:[EMAIL PROTECTED]
] On Behalf Of vivek sharma
Sent: 07 November 2008 09:00
To: Discussion list for GROMACS users
Subject: [gmx-users] Running MDS over docked poses

 Hi There,
I am trying to run MDS over some docked result generated by
Autodock4, but I am not sure of the forcefield I should use.
If anybody have tried doing it before, please guide me for the same.
For generating topology of ligand, I am using PRODRG server, which
has limited option for forcefield.
Also, how can I give the parameters for varying temperature of a
particular group during the MDS, like how canI define the steps I
want to vary it ?

waiting for some suggestion.

With Thanks,
Vivek
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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] about porse.itp




Bhawana Gupta wrote:

Dear gmx-users,

i made earlier asked this question .but there is a problem.
 first i got the error:
---
Program grompp, VERSION 4.0
Source code file: futil.c, line: 527

Fatal error:
Library file posre.itp not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)

Then on your advice, i put posre.itp in my directory, but i again got an 
error.


---
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 1196

Fatal error:
[ file posre.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section 
"position_restraints"

in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
---


Interestingly, this exact question was asked just a few days ago:

http://www.gromacs.org/pipermail/gmx-users/2008-November/037675.html

It would serve you well to search the archives; many answers can be found there. 
 And furthermore, grompp is giving you advice about how to solve the problem. 
Something in your .top is out of order.






then i again make a posre.itp file , which i like this
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.

[ position_restraints ]
; atom  type  fx  fy  fz

AFTER THAT I GOT NO ERROR.
TELL ME WHETHER I AM CORRECT AT THIS POINT.



Well, then you're applying no position restraints, which I suppose is not what 
you are after.


-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] prodrg




Bhawana Gupta wrote:

hello everyone,
 
Pls tell me whether we can use PRODRG server only for generating 
peptides with unusual amino acid through JME or it can be used for the 
peptides having usual amino acid.


PRODRG is most useful in obtaining topologies for small molecules.  You might 
use it to get the initial topology for an unusual amino acid, but you would 
probably be best to translate that topology into an .rtp file for yourself.


Be aware that the charges and charge groups generated by PRODRG typically 
require refinement and thorough validation of the parameters.


whether it is necessary to use pdb2gmx for peptide containing usual 
amino acid or we can do it with PRODRG server also.
 


Well, you could write your topology by hand, if you really wanted to :)  But 
pdb2gmx makes life quite simple for generating topologies of proteins and peptides.


-Justin


Pls help me out.
 
Bhawana





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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] Misunderstandings with g_rms

2008-11-07 Thread Jochen Hub

DimitryASuplatov wrote:
> Hello,
> 
> I am sorry for this stupid question.
> 
> Lets say I have an index file of all chain A atoms. I want to calculate
> RMS of chain A _backbone_ only.
> 
> I run g_rms. It asks two questions:
> 1/ Select group for least squares fit
> 2/ Select group for RMSD calculation
> 
> To the best of my understanding, I should answer "BACKBONE" to the first
> question and enter group number corresponding to chain A index file to
> the second one.

In your case you need to make an index file with a group of the backbone
of chain a, do something like

make_ndx -f x.gro
chain a
"ChA" & Backbone
q

then run g_rms with -n

And give the ChainA-backbone group twice to g_rms.

Best, Jochen

> 
> Is that correct?
> Thank you. 
> SDA 
> 
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> 
> .
> 

-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] Running MDS over docked poses

2008-11-07 Thread vivek sharma

Hi Andreas,
 Thanks for your response.
But I am not finding option for AMBER forcefield in gromacs (during pdb2gmx
step). which of the 9 force-field I should use for the same.

With Thanks,
Vivek

2008/11/7 Kukol, Andreas <[EMAIL PROTECTED]>

> Hi,
>
> Autodock4 uses the AMBER forcefield, so that would be a good starting point
> for gromacs as well.
>
> In order to set the temperature for a particular group
> 1) you generate an index file containing all the atoms in your GROUP
> 2) in your mdp-file specify GROUP as a separate temperature coupling group
> and specify the temperature you want
> 3) use grompp with -n yourindexfile.ndx
>
> Note sure, if this is makes physically sense though.
>
> Andreas
>
>
> >
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of vivek sharma
> Sent: 07 November 2008 09:00
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Running MDS over docked poses
>
>  Hi There,
> I am trying to run MDS over some docked result generated by Autodock4, but
> I am not sure of the forcefield I should use.
> If anybody have tried doing it before, please guide me for the same. For
> generating topology of ligand, I am using PRODRG server, which has limited
> option for forcefield.
> Also, how can I give the parameters for varying temperature of a particular
> group during the MDS, like how canI define the steps I want to vary it ?
>
> waiting for some suggestion.
>
> With Thanks,
> Vivek
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Re: [gmx-users] missing of methyl at N-terminal




Bhawana Gupta wrote:

thankyou for ur reply.
exact error which i m getting, when running pdb2gmx command with the pdb 
which i had taken from insightII is

Program pdb2gmx, VERSION 4.0
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C in residue NH2 6 not found in rtp entry with 3 atoms
 while sorting atoms



This probably comes about because you are trying to use parameters from an -NH2 
group on a structure that contains -NH(CH3).  You also haven't mentioned which 
force field you're trying to use.  Some force fields do not have an N-methyl 
group parameterized (check the .rtp file).


-Justin



this is my pdb in text editor
there is a presence of 25 atom in my pdb (C in residue NH2 6), but i m 
getting the error mentioned above

AUTHORGENERATED BY OPEN BABEL 2.2.0
ATOM  1  CA  ACE 1  -3.811  -0.502   0.471  1.00  
0.00   C  
ATOM  2  C   ACE 1  -2.354  -0.410   0.072  1.00  
0.00   C  
ATOM  3  O   ACE 1  -1.743  -1.403  -0.345  1.00  
0.00   O  
ATOM  4  N   ALA 2  -1.649   0.885   0.183  1.00  
0.00   N  
ATOM  5  CA  ALA 2  -0.244   1.035  -0.187  1.00  
0.00   C  
ATOM  6  C   ALA 2   0.221   2.456   0.023  1.00  
0.00   C  
ATOM  7  O   ALA 2  -0.530   3.334   0.466  1.00  
0.00   O  
ATOM  8  CB  ALA 2  -0.094   0.568  -1.645  1.00  
0.00   C  
ATOM  9  N   ALA 3   1.482   2.703  -0.281  1.00  
0.00   N  
ATOM 10  CA  ALA 3   2.069   4.031  -0.129  1.00  
0.00   C  
ATOM 11  C   ALA 3   3.519   4.033  -0.548  1.00  
0.00   C  
ATOM 12  O   ALA 3   4.081   3.015  -0.969  1.00  
0.00   O  
ATOM 13  CB  ALA 3   1.870   4.463   1.334  1.00  
0.00   C  
ATOM 14  N   ALA 4   4.149   5.189  -0.449  1.00  
0.00   N  
ATOM 15  CA  ALA 4   5.553   5.340  -0.819  1.00  
0.00   C  
ATOM 16  C   ALA 4   6.019   6.761  -0.609  1.00  
0.00   C  
ATOM 17  O   ALA 4   5.267   7.638  -0.166  1.00  
0.00   O  
ATOM 18  CB  ALA 4   5.704   4.872  -2.277  1.00  
0.00   C  
ATOM 19  N   ALA 5   7.279   7.008  -0.913  1.00  
0.00   N  
ATOM 20  CA  ALA 5   7.866   8.336  -0.760  1.00  
0.00   C  
ATOM 21  C   ALA 5   9.317   8.337  -1.179  1.00  
0.00   C  
ATOM 22  O   ALA 5   9.879   7.319  -1.601  1.00  
0.00   O  
ATOM 23  CB  ALA 5   7.668   8.768   0.703  1.00  
0.00   C  
ATOM 24  N   NHM 6  10.022   9.633  -1.069  1.00  
0.00   N  
ATOM 25  C   NHM 6  11.417   9.736  -1.462  1.00  
0.00   C 
CONECT12  
CONECT2341
CONECT32  
CONECT452 
CONECT5864
CONECT6957
CONECT76  
CONECT85  
CONECT9   106 
CONECT   10   119   13
CONECT   11   12   14   10
CONECT   12   11  
CONECT   13   10  
CONECT   14   15   11 
CONECT   15   18   16   14
CONECT   16   19   15   17
CONECT   17   16  
CONECT   18   15  
CONECT   19   20   16 
CONECT   20   21   19   23
CONECT   21   22   24   20
CONECT   22   21  
CONECT   23   20  
CONECT   24   25   21 
CONECT   25   24  
MASTER00000000   250   250

END

Please help me out.

With regards
Bhawana




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[gmx-users] Spatial distribution

2008-11-07 Thread Gadzikano Munyuki

I want to analyse the solvent around a peptide . I used g_sdf and the output  
that i am getting (i.e the refmol.gro) does not have the whole peptide molecule 
but just the residues that i use to define the coordinate system . I then tried 
to use g_spatialbut its doing something very different and not spatial 
distibution, it looks like  its executing g_cluster instead. I was wondering if 
g_custer and g_spatial are meant to do the same thing.

Gadzikano


 

 
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[gmx-users] Misunderstandings with g_rms

2008-11-07 Thread DimitryASuplatov

Hello,

I am sorry for this stupid question.

Lets say I have an index file of all chain A atoms. I want to calculate
RMS of chain A _backbone_ only.

I run g_rms. It asks two questions:
1/ Select group for least squares fit
2/ Select group for RMSD calculation

To the best of my understanding, I should answer "BACKBONE" to the first
question and enter group number corresponding to chain A index file to
the second one.

Is that correct?
Thank you. 
SDA 

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[gmx-users] about porse.itp

Dear gmx-users,

i made earlier asked this question .but there is a problem.
 first i got the error:
---
Program grompp, VERSION 4.0
Source code file: futil.c, line: 527

Fatal error:
Library file posre.itp not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)

Then on your advice, i put posre.itp in my directory, but i again got an
error.

---
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 1196

Fatal error:
[ file posre.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
---
This is the porse file which i have included.
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom  type  fx  fy  fz
 1 1  1000  1000  1000
 3 1  1000  1000  1000
 5 1  1000  1000  1000
 6 1  1000  1000  1000
 7 1  1000  1000  1000
 8 1  1000  1000  1000
 9 1  1000  1000  1000
10 1  1000  1000  1000
13 1  1000  1000  1000
14 1  1000  1000  1000
15 1  1000  1000  1000
17 1  1000  1000  1000
18 1  1000  1000  1000
19 1  1000  1000  1000
20 1  1000  1000  1000
21 1  1000  1000  1000
22 1  1000  1000  1000
26 1  1000  1000  1000
27 1  1000  1000  1000
28 1  1000  1000  1000
30 1  1000  1000  1000
31 1  1000  1000  1000
32 1  1000  1000  1000
33 1  1000  1000  1000
34 1  1000  1000  1000
35 1  1000  1000  1000
36 1  1000  1000  1000
37 1  1000  1000  1000
39 1  1000  1000  1000
40 1  1000  1000  1000
41 1  1000  1000  1000
42 1  1000  1000  1000
43 1  1000  1000  1000
44 1  1000  1000  1000
45 1  1000  1000  1000
47 1  1000  1000  1000
48 1  1000  1000  1000
49 1  1000  1000  1000
50 1  1000  1000  1000
52 1  1000  1000  1000
54 1  1000  1000  1000
56 1  1000  1000  1000
58 1  1000  1000  1000
60 1  1000  1000  1000
61 1  1000  1000  1000
62 1  1000  1000  1000
64 1  1000  1000  1000
65 1  1000  1000  1000
66 1  1000  1000  1000
67 1  1000  1000  1000
69 1  1000  1000  1000
71 1  1000  1000  1000
73 1  1000  1000  1000
75 1  1000  1000  1000
77 1  1000  1000  1000
78 1  1000  1000  1000
79 1  1000  1000  1000
81 1  1000  1000  1000
82 1  1000  1000  1000
83 1  1000  1000  1000
84 1  1000  1000  1000
85 1  1000  1000  1000
87 1  1000  1000  1000
88 1  1000  1000  1000
89 1  1000  1000  1000
90 1  1000  1000  1000
91 1  1000  1000  1000
92 1  1000  1000  1000
93 1  1000  1000  1000
94 1  1000  1000  1000
95 1  1000  1000  1000
97 1  1000  1000  1000
98 1  1000  1000  1000
99 1  1000  1000  1000
   100 1  1000  1000  1000
   101 1  1000  1000  1000
   102 1  1000  1000  1000
   103 1  1000  1000  1000
   104 1  1000  1000  1000
   106 1  1000  1000  1000
   107 1  1000  1000  1000
   108 1  1000  1000  1000
   109 1  1000  1000  1000
   110 1  1000  1000  1000
   111 1  1000  1000  1000
   112 1  1000  1000  1000
   114 1  1000  1000  1000
   115 1  1000  1000  1000
   116 1  1000  1000  1000
   117 1  1000  1000  1000
   119 1  1000  1000  1000
   120 1  1000  1000  1000
   121 1  1000  1000  1000
   123 1  1000  1000  1000
   124 1  1000  1000  1000
   125 1  1000  1000  1000
   127 1  1000  1000  1000
   128 1  1000  1000  1000
   129 1  1000  1000  1000
   130 1  1000  1000  1000
   131 1  1000  1000  1000
   134 1  1000  1000  1000
   135 1  1000  1000  1000
   136 1  1000  1000  1000
   138 1  1000  1000  1000
   139 1  1000  1000  1000
   140 1  1000  1000  1000


then i again make a posre.itp file , which i like this
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.

[ position_restraints ]
; atom  type  fx  fy  fz

AFTER THAT I GOT NO ERROR.
TELL ME WHETHER I AM CORRECT AT THIS POINT.
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Re: [gmx-users] editconf/genbox problem in Gromacs 4.0

2008-11-07 Thread Caterina Arcangeli

Right!
Thanks again Berk.
Caterina

2008/11/7 Berk Hess <[EMAIL PROTECTED]>:
> Hi,
>
> For the moment you can use editconf of 3.3
> or copy a cryst1 entry (one of the first lines) from another pdb file
> into you pdb input file, editconf will then write the correct box in the
> output pdb.
>
> Berk
>
>
>> Date: Fri, 7 Nov 2008 12:13:55 +0100
>> From: [EMAIL PROTECTED]
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] editconf/genbox problem in Gromacs 4.0
>>
>> Many thanks to Bert and Xavier.
>>
>> >> Dear gmx-users,
>> >>
>> >> I have encountered a similar editconf/genbox problem posted by Matt
>> >> Danielson on 14 October:
>> >> I 'm using Gromacs 4.0 (installed on MacOS).
>> >>
>> >> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o
>> >> may_protein_box.pdb
>> >
>> > use gro files for output and it works. The box size is not written
>> > in the pdb file, although it used to be.
>> >>
>>
>> Yes, it works, but I'm using .pdb instead of .gro format to support
>> chain identifiers since my system is composed by 3 protein chains.
>> So I will wait for the new 4.0.1 release.
>>
>> Caterina
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RE: [gmx-users] editconf/genbox problem in Gromacs 4.0

2008-11-07 Thread Berk Hess


Hi,

For the moment you can use editconf of 3.3
or copy a cryst1 entry (one of the first lines) from another pdb file
into you pdb input file, editconf will then write the correct box in the output 
pdb.

Berk


> Date: Fri, 7 Nov 2008 12:13:55 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] editconf/genbox problem in Gromacs 4.0
> 
> Many thanks to Bert and Xavier.
> 
> >> Dear gmx-users,
> >>
> >> I have encountered a similar editconf/genbox problem posted by Matt
> >> Danielson on 14 October:
> >> I 'm using Gromacs 4.0 (installed on MacOS).
> >>
> >> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o
> >> may_protein_box.pdb
> >
> > use gro files for output and it works. The box size is not written
> > in the pdb file, although it used to be.
> >>
> 
> Yes, it works, but I'm using .pdb instead of .gro format to support
> chain identifiers since my system is composed by 3 protein chains.
> So I will wait for the new 4.0.1 release.
> 
> Caterina
> ___
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Re: [gmx-users] editconf/genbox problem in Gromacs 4.0

2008-11-07 Thread Caterina Arcangeli

Many thanks to Bert and Xavier.

>> Dear gmx-users,
>>
>> I have encountered a similar editconf/genbox problem posted by Matt
>> Danielson on 14 October:
>> I 'm using Gromacs 4.0 (installed on MacOS).
>>
>> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o
>> may_protein_box.pdb
>
> use gro files for output and it works. The box size is not written
> in the pdb file, although it used to be.
>>

Yes, it works, but I'm using .pdb instead of .gro format to support
chain identifiers since my system is composed by 3 protein chains.
So I will wait for the new 4.0.1 release.

Caterina
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[gmx-users] prodrg

hello everyone,

Pls tell me whether we can use PRODRG server only for generating peptides
with unusual amino acid through JME or it can be used for the peptides
having usual amino acid.
whether it is necessary to use pdb2gmx for peptide containing usual amino
acid or we can do it with PRODRG server also.

Pls help me out.

Bhawana
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Re: [gmx-users] editconf/genbox problem in Gromacs 4.0

2008-11-07 Thread Xavier Periole


On Fri, 7 Nov 2008 11:23:14 +0100
 "Caterina Arcangeli" <[EMAIL PROTECTED]> wrote:

Dear gmx-users,

I have encountered a similar editconf/genbox problem posted by Matt
Danielson on 14 October:
I 'm using Gromacs 4.0 (installed on MacOS).

1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o 
may_protein_box.pdb

use gro files for output and it works. The box size is not written
in the pdb file, although it used to be.


The output from editconf does not report errors, but I noted that the
volume of the box is 0!

--- output message---
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Entries in vdwradii.dat: 28
Entries in dgsolv.dat: 7
Entries in electroneg.dat: 71
Entries in elements.dat: 218
Read 16824 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
-

2. genbox_d -cp my_protein_box.pdb -cs spc216.gro  -o
my_protein_wat.pdb -p my_protein.top

The output from genbox_d reports the following error:
---
Program genbox, VERSION 4.0
Source code file: gmx_genbox.c, line: 744

Fatal error:
Undefined solute box.
Create one with editconf or give explicit -box command line option
---


I have performed the same commands on another machine (Linux) running
version 3.3 and I produced with success a nice solvent box.

Suggestions?

Thanks,
Caterina



--
Caterina Arcangeli
ENEA, Dept. Physics (FIM-CAMO)
C.R. Casaccia, SP 026
Via Anguillarese 301 - 00123 Roma
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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] editconf/genbox problem in Gromacs 4.0

2008-11-07 Thread Berk Hess


Hi,

This is a known bug in 4.0.
It has been fixed for 4.0.1, which will hopefully be released today.

Berk


> Date: Fri, 7 Nov 2008 11:23:14 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] editconf/genbox problem in Gromacs 4.0
> 
> Dear gmx-users,
> 
> I have encountered a similar editconf/genbox problem posted by Matt
> Danielson on 14 October:
> I 'm using Gromacs 4.0 (installed on MacOS).
> 
> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o 
> may_protein_box.pdb
> 
> The output from editconf does not report errors, but I noted that the
> volume of the box is 0!
> 
> --- output message---
> WARNING: masses will be determined based on residue and atom names,
>  this can deviate from the real mass of the atom type
> Entries in atommass.dat: 178
> WARNING: vdwradii will be determined based on residue and atom names,
>  this can deviate from the real mass of the atom type
> Entries in vdwradii.dat: 28
> Entries in dgsolv.dat: 7
> Entries in electroneg.dat: 71
> Entries in elements.dat: 218
> Read 16824 atoms
> Volume: 0 nm^3, corresponds to roughly 0 electrons
> -
> 
> 2. genbox_d -cp my_protein_box.pdb -cs spc216.gro  -o
> my_protein_wat.pdb -p my_protein.top
> 
> The output from genbox_d reports the following error:
> ---
> Program genbox, VERSION 4.0
> Source code file: gmx_genbox.c, line: 744
> 
> Fatal error:
> Undefined solute box.
> Create one with editconf or give explicit -box command line option
> ---
> 
> 
> I have performed the same commands on another machine (Linux) running
> version 3.3 and I produced with success a nice solvent box.
> 
> Suggestions?
> 
> Thanks,
> Caterina
> 
> 
> 
> -- 
> Caterina Arcangeli
> ENEA, Dept. Physics (FIM-CAMO)
> C.R. Casaccia, SP 026
> Via Anguillarese 301 - 00123 Roma
> ___
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[gmx-users] editconf/genbox problem in Gromacs 4.0

2008-11-07 Thread Caterina Arcangeli

Dear gmx-users,

I have encountered a similar editconf/genbox problem posted by Matt
Danielson on 14 October:
I 'm using Gromacs 4.0 (installed on MacOS).

1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb

The output from editconf does not report errors, but I noted that the
volume of the box is 0!

--- output message---
WARNING: masses will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Entries in vdwradii.dat: 28
Entries in dgsolv.dat: 7
Entries in electroneg.dat: 71
Entries in elements.dat: 218
Read 16824 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
-

2. genbox_d -cp my_protein_box.pdb -cs spc216.gro  -o
my_protein_wat.pdb -p my_protein.top

The output from genbox_d reports the following error:
---
Program genbox, VERSION 4.0
Source code file: gmx_genbox.c, line: 744

Fatal error:
Undefined solute box.
Create one with editconf or give explicit -box command line option
---


I have performed the same commands on another machine (Linux) running
version 3.3 and I produced with success a nice solvent box.

Suggestions?

Thanks,
Caterina



-- 
Caterina Arcangeli
ENEA, Dept. Physics (FIM-CAMO)
C.R. Casaccia, SP 026
Via Anguillarese 301 - 00123 Roma
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Re: [gmx-users] missing of methyl at N-terminal

thankyou for ur reply.
exact error which i m getting, when running pdb2gmx command with the pdb
which i had taken from insightII is
Program pdb2gmx, VERSION 4.0
Source code file: pdb2gmx.c, line: 429

Fatal error:
Atom C in residue NH2 6 not found in rtp entry with 3 atoms
 while sorting atoms


this is my pdb in text editor
there is a presence of 25 atom in my pdb (C in residue NH2 6), but i m
getting the error mentioned above
AUTHORGENERATED BY OPEN BABEL 2.2.0
ATOM  1  CA  ACE 1  -3.811  -0.502   0.471  1.00  0.00
C
ATOM  2  C   ACE 1  -2.354  -0.410   0.072  1.00  0.00
C
ATOM  3  O   ACE 1  -1.743  -1.403  -0.345  1.00  0.00
O
ATOM  4  N   ALA 2  -1.649   0.885   0.183  1.00  0.00
N
ATOM  5  CA  ALA 2  -0.244   1.035  -0.187  1.00  0.00
C
ATOM  6  C   ALA 2   0.221   2.456   0.023  1.00  0.00
C
ATOM  7  O   ALA 2  -0.530   3.334   0.466  1.00  0.00
O
ATOM  8  CB  ALA 2  -0.094   0.568  -1.645  1.00  0.00
C
ATOM  9  N   ALA 3   1.482   2.703  -0.281  1.00  0.00
N
ATOM 10  CA  ALA 3   2.069   4.031  -0.129  1.00  0.00
C
ATOM 11  C   ALA 3   3.519   4.033  -0.548  1.00  0.00
C
ATOM 12  O   ALA 3   4.081   3.015  -0.969  1.00  0.00
O
ATOM 13  CB  ALA 3   1.870   4.463   1.334  1.00  0.00
C
ATOM 14  N   ALA 4   4.149   5.189  -0.449  1.00  0.00
N
ATOM 15  CA  ALA 4   5.553   5.340  -0.819  1.00  0.00
C
ATOM 16  C   ALA 4   6.019   6.761  -0.609  1.00  0.00
C
ATOM 17  O   ALA 4   5.267   7.638  -0.166  1.00  0.00
O
ATOM 18  CB  ALA 4   5.704   4.872  -2.277  1.00  0.00
C
ATOM 19  N   ALA 5   7.279   7.008  -0.913  1.00  0.00
N
ATOM 20  CA  ALA 5   7.866   8.336  -0.760  1.00  0.00
C
ATOM 21  C   ALA 5   9.317   8.337  -1.179  1.00  0.00
C
ATOM 22  O   ALA 5   9.879   7.319  -1.601  1.00  0.00
O
ATOM 23  CB  ALA 5   7.668   8.768   0.703  1.00  0.00
C
ATOM 24  N   NHM 6  10.022   9.633  -1.069  1.00  0.00
N
ATOM 25  C   NHM 6  11.417   9.736  -1.462  1.00  0.00
C
CONECT12
CONECT2341
CONECT32
CONECT452
CONECT5864
CONECT6957
CONECT76
CONECT85
CONECT9   106
CONECT   10   119   13
CONECT   11   12   14   10
CONECT   12   11
CONECT   13   10
CONECT   14   15   11
CONECT   15   18   16   14
CONECT   16   19   15   17
CONECT   17   16
CONECT   18   15
CONECT   19   20   16
CONECT   20   21   19   23
CONECT   21   22   24   20
CONECT   22   21
CONECT   23   20
CONECT   24   25   21
CONECT   25   24
MASTER00000000   250   250
END

Please help me out.

With regards
Bhawana
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RE: [gmx-users] Running MDS over docked poses

2008-11-07 Thread Kukol, Andreas

Hi,

Autodock4 uses the AMBER forcefield, so that would be a good starting point for 
gromacs as well.

In order to set the temperature for a particular group
1) you generate an index file containing all the atoms in your GROUP
2) in your mdp-file specify GROUP as a separate temperature coupling group and 
specify the temperature you want
3) use grompp with -n yourindexfile.ndx

Note sure, if this is makes physically sense though.

Andreas


>
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of vivek sharma
Sent: 07 November 2008 09:00
To: Discussion list for GROMACS users
Subject: [gmx-users] Running MDS over docked poses

 Hi There,
I am trying to run MDS over some docked result generated by Autodock4, but I am 
not sure of the forcefield I should use.
If anybody have tried doing it before, please guide me for the same. For 
generating topology of ligand, I am using PRODRG server, which has limited 
option for forcefield.
Also, how can I give the parameters for varying temperature of a particular 
group during the MDS, like how canI define the steps I want to vary it ?

waiting for some suggestion.

With Thanks,
Vivek
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[gmx-users] Running MDS over docked poses

2008-11-07 Thread vivek sharma

 Hi There,
I am trying to run MDS over some docked result generated by Autodock4, but I
am not sure of the forcefield I should use.
If anybody have tried doing it before, please guide me for the same. For
generating topology of ligand, I am using PRODRG server, which has limited
option for forcefield.
Also, how can I give the parameters for varying temperature of a particular
group during the MDS, like how canI define the steps I want to vary it ?

waiting for some suggestion.

With Thanks,
Vivek
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Re: [gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)


Chih-Ying Lin wrote:

HI
BR- ion is defined in FF_OPLS.
Could I mix two force fields, FF_Gromos 96 and FF_OPLS, in my system?


; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
opls_402   Br- 35   79.90400-1.000   A4.62376e-01  3.76560e-01


Does it make sense?


No. See http://wiki.gromacs.org/index.php/Force_Fields

Mark
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[gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)

2008-11-07 Thread Chih-Ying Lin

HI
BR- ion is defined in FF_OPLS.
Could I mix two force fields, FF_Gromos 96 and FF_OPLS, in my system?


; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
opls_402   Br- 35   79.90400-1.000   A4.62376e-01  3.76560e-01


Does it make sense?

Thank you
Lin








Chih-Ying Lin wrote:
> Hi
> In the ions.itp, there is no BR- ion defined  (FF_Gromos 96).
>
> But, it was defined in FF_OPLS.
>
> How did people solve the problem?
> Could I simply use all of  BR-atom (assign it a -1 charge) non-bonded
> parameters in FF_Gromos96 instead?
>
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Re: [gmx-users] Water model => amber port to gromacs


Chih-Ying Lin wrote:

Hi
Water model => amber port to gromacs

The two steps are shown on the archive.
1. #include ffamber_tip*pin the .top file
2. include an #ifdef_FF_AMBER statement in tip*p.itp


If you want others' opinions for free, please provide links - and test 
them first to see that you've linked to the content, and not some 
wrapper page/frame! :-)



Should I also #include ffamber99.tip in the .top file?


"tip" does not equal "itp" :-)

Mark
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Re: [gmx-users] missing of methyl at N-terminal