Re: [gmx-users] XRAMA\environment variable\

2006-12-14 Thread David van der Spoel

Bio wrote:

Hello sapiens,

Thanks for ur previous suggestions.  While we are trying to view
ramachandran movie through xrama, we have got  error as can't open
display, set your DISPLAY environment variable.Let us come to know how
to fix this problem.we are running GROMACS in winXP with cygwin.

Thank You,
Regards
E.Elavazhagan.

Do you have a running X server?


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] problem with genbox

2006-12-14 Thread David van der Spoel

Li, Yun wrote:

Thanks for getting back to me so quickly. I am following this tutorial:
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm

It seems to be very straight forward. However, I can't overcome my
problem. Here is the output from genbox: 


 :-)  G  R  O  M  A  C  S  (-:

   GRowing Old MAkes el Chrono Sweat

:-)  VERSION 3.1.2  (-:


You're using a prehistoric version of gromacs. I'm not sure how well 
that should work in Windows. It seems that there is a problem with file 
handling that could be OS specific (but none of the developers works 
with Windows). The output from genbox looks fine.


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] XRAMA\environment variable\

2006-12-14 Thread Bio
Hello sapiens,

Thanks for ur previous suggestions.  While we are trying to view
ramachandran movie through xrama, we have got  error as can't open
display, set your DISPLAY environment variable.Let us come to know how
to fix this problem.we are running GROMACS in winXP with cygwin.

Thank You,
Regards
E.Elavazhagan.
-- 
  Bio
  [EMAIL PROTECTED]

-- 
http://www.fastmail.fm - Does exactly what it says on the tin

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RE: [gmx-users] problem with genbox

2006-12-14 Thread Li, Yun
Thanks for getting back to me so quickly. I am following this tutorial:
http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm

It seems to be very straight forward. However, I can't overcome my
problem. Here is the output from genbox: 

 :-)  G  R  O  M  A  C  S  (-:

   GRowing Old MAkes el Chrono Sweat

:-)  VERSION 3.1.2  (-:


   Copyright (c) 1991-2002, University of Groningen, The Netherlands
 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

   :-)  c:\Program Files\Gromacs\bin\genbox.exe  (-:

Option Filename  Type  Description

 -cpbox.pdb  Input, Opt!   Generic structure: gro g96 pdb tpr
tpb tpa
 -cs spc216.gro  Input, Opt!, Lib.  Generic structure: gro g96 pdb
tpr tpb
   tpa
 -ci insert.gro  Input, Opt.   Generic structure: gro g96 pdb tpr
tpb tpa
  -o  water.pdb  OutputGeneric structure: gro g96 pdb
  -p  topol.top  In/Out, Opt!  Topology file

Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 12298 charge groups and 12298 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Grid: 18 x 14 x 20 cells
Adding line for 2164 solute molecules to topology file (topol.top)
  Option   Type  Value  Description
--
  -[no]h   bool no  Print help info and quit
  -[no]X   bool no  Use dialog box GUI to edit command line
options
   -niceint 19  Set the nicelevel
-box vector  0 0 0  box size
   -nmolint  0  no of extra molecules to insert
-tryint 10  try inserting -nmol*-try times
   -seedint   1997  random generator seed
   -vdwd   real  0.105  default vdwaals distance
  -shell   real  0  thickness of optional water layer around
solute

Reading solute configuration
PROTEIN G (B1 IGG-BINDING DOMAIN)
Containing 634 atoms in 80 residues
Initialising van der waals distances...
Opening library file C:\Program Files\Gromacs\share\top\vdwradii.dat
Opening library file C:\Program Files\Gromacs\share\top\aminoacids.dat
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 3x2x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL (   3 atoms):  3888 residues
Calculating Overlap...
box_margin = 0.315
Removed 2868 atoms that were outside the box
Succesfully made neighbourlist
nri = 20556, nrj = 531741
Checking Protein-Solvent overlap: tested 13099 pairs, removed 960 atoms.
Checking Solvent-Solvent overlap: tested 120781 pairs, removed 1416
atoms.
Added 2140 molecules
Generated solvent containing 6420 atoms in 2140 residues
Writing generated configuration to water.pdb

Back Off! I just backed up water.pdb to ./#water.pdb.5#
PROTEIN G (B1 IGG-BINDING DOMAIN)

Output configuration contains 7054 atoms in 2220 residues
WARNING: masses will be determined based on residue and atom names,
 this can deviate from the real mass of the atom type
Opening library file C:\Program Files\Gromacs\share\top\atommass.dat
Volume : 75.6474 (nm^3)
Density: 991.464 (g/l)
Number of SOL molecules:   2164   

Processing topology

Back Off! I just backed up temp.top to ./#temp.top.5#

Back Off! I just backed up topol.top to ./#topol.top.6#

gcq#115: "A Lady Shaves Her Legs" (C. Meijering)


Yun Li
 
Assistant Professor of Chemistry
Delaware Valley College
700 E. Butler Ave.,
Doylestown, PA 18901
(215) 489-2482

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Re: [gmx-users] problem with genbox

2006-12-14 Thread Mark Abraham

Li, Yun wrote:

Hi,

 

I was very excited to discover Gromacs and decided to learn by following 
a few tutorials I found online. However, I ran into a problem: After 
filling up the simulation box with SPC water using genbox, the program 
backed up the topology file into another file with its name flanked by 
#, and left me with an empty topology file. 


Read carefully the output from genbox - I expect there's an error there 
that you've missed.


Without knowing what had 
happened I went ahead and ran grompp, which exited with a fatal error, 
saying the number of atoms in the topology file does not match that of 
the coordinate file. I tried to use the backed up topology file, or to 
generate a new topology file using pdb2gmx, but ended up with the same 
error message. Grompp thinks there is no atom in the topology files.


Well, of course it will, if the .top file is empty!

Does anyone know what is going on? Also, water molecules don’t seem to 
appear in topology files. Does that matter?


They get pulled in with the #include mechanism.

The general structure of a .top file is a series of [ moleculetype ] 
sections, followed by a [ system ] section that describes the system as 
a set of the predefined molecules. For water, the [ moleculetype ] 
sections are contained in an .itp file that gets included by cpp. Your 
solute is in the .top file directly, in the usual case. Please read 
Chapter 5 fof the manual or more info.


Mark
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Re: [gmx-users] PME error in gromacs-3.3.1

2006-12-14 Thread Mark Abraham

Yuhui Li wrote:

Hi, all

I installed gromacs-3.3.1 recently and tested a system consisting only 
thress water molecules. When I use coulombtype = Cut-off, it works well, 
but if I use coulombtype = PME, there was a segmentation fault. I have 
checked the maillist archives and found that some people had the same 
problem in gromacs-3.3. From their instruction, the new pme.c file was 
tried and   pme_order = 4 was set, but the problem is still there. Do 
you have idea about this problem?


Actually, if you mean only "three" water molecules, the problem is 
likely to be that the fftw grid interpolation will fail if there is not 
at least one something per something (can't remember, check the archives 
if you care). Try doing a system of reasonable size.


Mark
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Re: [gmx-users] PME error in gromacs-3.3.1

2006-12-14 Thread Mark Abraham

Yuhui Li wrote:

Hi, all

I installed gromacs-3.3.1 recently and tested a system consisting only 
thress water molecules. When I use coulombtype = Cut-off, it works well, 
but if I use coulombtype = PME, there was a segmentation fault. I have 
checked the maillist archives and found that some people had the same 
problem in gromacs-3.3. From their instruction, the new pme.c file was 
tried and   pme_order = 4 was set, but the problem is still there. Do 
you have idea about this problem?


No, that problem is fixed in 3.3.1.

I expect there is a problem with the installation of your fftw 
libraries.. I suggest you do a make clean, do configure again, and make 
install.


Mark
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[gmx-users] problem with genbox

2006-12-14 Thread Li, Yun
Hi,

 

I was very excited to discover Gromacs and decided to learn by following
a few tutorials I found online. However, I ran into a problem: After
filling up the simulation box with SPC water using genbox, the program
backed up the topology file into another file with its name flanked by
#, and left me with an empty topology file. Without knowing what had
happened I went ahead and ran grompp, which exited with a fatal error,
saying the number of atoms in the topology file does not match that of
the coordinate file. I tried to use the backed up topology file, or to
generate a new topology file using pdb2gmx, but ended up with the same
error message. Grompp thinks there is no atom in the topology files.

 

Does anyone know what is going on? Also, water molecules don't seem to
appear in topology files. Does that matter?

 

Thank you very much if you have read this much. Any idea what's going
on. Your help will be greatly appreciated.

 

Yun Li

 

Assistant Professor of Chemistry

Delaware Valley College

700 E. Butler Ave.,

Doylestown, PA 18901

(215) 489-2482

 

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[gmx-users] PME error in gromacs-3.3.1

2006-12-14 Thread Yuhui Li

Hi, all

I installed gromacs-3.3.1 recently and tested a system consisting only
thress water molecules. When I use coulombtype = Cut-off, it works well, but
if I use coulombtype = PME, there was a segmentation fault. I have checked
the maillist archives and found that some people had the same problem in
gromacs-3.3. From their instruction, the new pme.c file was tried and
pme_order = 4 was set, but the problem is still there. Do you have idea
about this problem?

Thank you!

--
Yuhui
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Re: [gmx-users] Dipolar correlation function

2006-12-14 Thread chiradip chatterjee
Hi David
Thanks for your reply. I want to calculate dipolar
corelation function C(t) between proton and fluorine
using the equation:

C(t) = 1/4Σ[(3cos2θ(0)-1
)(3cos2θ(t)-1 )]/r(0)r3(t)

(ref Fellar et al, JACS 121, 8963-64, 1999)

where I have a proton i and total n fluorines. At time
= 0, a proton-fluorine vector has a length  r(0) and
is oriented at an angle θ(0) relative to the
z-axis. At a time t later in the trajectory the vector
has length  r(t) and is oriented at an angle 
θ(t) relative to the z-axis. Is there any way to
get the plot of the average C(t) vs time (ps)?
Thanks in advance 
Chiradip



--- David van der Spoel <[EMAIL PROTECTED]> wrote:

> chiradip chatterjee wrote:
> > Hi gmx user,
> > Is there any way in gromacs to compute dipolar
> > correlation function between solvent atom and one
> atom
> > of my protein from trajectory data? I went through
> > g_rotacf with -d option. But I think it gives 
> > rotational correlation function for linear
> molecules
> > by specifying two atoms (i,j) in the index file
> that
> > means two atoms i-j with a bond.
> > Is g_dipole -corr is an option?
> > please advice me.
> > Chiradip
> > 
> Please be more specific, what do you want to
> compute? Please give an 
> equation.
> 
> g_dipoles -corr computes a dipole vector from given
> atoms (e.g. a water 
> molecule) and computes it's rotational
> autocorrelation.
> 
> g_rotacf may do what you need, you don't need a
> bond, just a vector 
> between two atoms. However, if they diffuse apart
> more than half a box 
> periodic boundary conditions will kick in and give
> strange results...
> 
> -- 
> David.
>

> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:46 18 471 4205  fax: 46 18 511 755
> [EMAIL PROTECTED] [EMAIL PROTECTED]  
> http://folding.bmc.uu.se
>

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[gmx-users] Re: free energy calculation & TI

2006-12-14 Thread David Mobley

Anirban and all,

I am putting this on list since I don't want to make a full-time job
out of answering free energy questions (although stay tuned for a more
extensive tutorial) and hopefully I can avoid answering the same
question more than once.


I have seen your posts on gromacs mailing list regarding free
energy calculation through TI and the need to partition the calculation
into two steps :

1. change in VDW only
2. change in electrostatics only


This isn't essential, but I think it's a good idea, at least in terms
of efficiency.


I was trying to run a free energy calculation run at lambda= and lambda=1
and I found that at lambda=1 my job blew up i.e. it showed LINCS warning
and
dumped stepxx.pdbs...could you tell me what might  be the reason? This
happened during stage 1 as mentioned above. In stage 2 the runs at
lambda=0 and lambda=1 stops after sometime...seems there is some
destabilizing forces.


By stage 2, you mean changing electrostatics? It would be helpful if
you could be more specific about the transformations you're doing, and
how. Any number of things could be going on:
(a) If, for example, you are doing things in a funny order (like first
turning off van der Waals interactions, and then modifying the
electrostatics) you may run into problems. (i.e. in that example, you
have the possibility of bare charges with opposite signs overlapping
with one another).
(b) If you are changing Lennard-Jones interactions without using soft
core, you can run into problems
(c) If you don't do adequate minimization or equilibration, you can
run into problems

Overall, you are basically getting forces that are too large for your
timestep for some particular reason. This could be related to the fact
that you're doing free energy calculations, or it could have nothing
to do with it. The basic solution is to figure out why you're getting
such large forces, and fix it (if it's a problem); otherwise, reduce
your timestep.


I have also seen some posts where three steps are mentioned for free
energy calculation..could you clarify on that ?


It will be helpful if you quote them or point me to them; I don't have
time to go through the archives to figure out what you're talking
about or how it applies here. Sorry. I'm happy to help if you can be
more specific.

Sorry this stuff is so scattered through the archives. One thing on my
to-do list is a "best practices" paper for free energy calculations
(which will initially be a wiki page, before I publish it). When I
pull that together, I will send an e-mail to the list so people can
refer to that rather than having to dig through the archives.

Best wishes,
David



thanks
anirban


Dr. Anirban Mudi
Postdoctoral Fellow
Biocomputing Group
Department of Biological Sciences
University of Calgary
2500 University Drive NW
Calgary AB
Canada T2N 1N4
(403) 220 6873
http://moose.bio.ucalgary.ca/



BE THE CHANGE YOU WISH TO SEE-> www.aidindia.org



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[gmx-users] How to implement dihedral restraints

2006-12-14 Thread chris . neale
I am not sure what you are asking since I believe that I have already  
given you this answer on the gromacs mailing list.  
http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html


I certainly do not mind personal emails and I am happy to help, but  
there are three very good reasons to keep everything on the gromacs  
mailing list:
1. Answers may be read by people who disagree with portions of the  
answer -- such as Mark's suggestion that my system's stability using a  
dihedral restraint around 180deg was fortuitous and that you should  
redefine your dihedral to avoid that.  
http://www.gromacs.org/pipermail/gmx-users/2006-December/025089.html

2. I may not know the answer to your question but somebody else might.
3. The questions and answers are maintained for somebody else to  
search through years later.


In fact, I don't know how to do exactly what you are suggesting. Do  
you mean that at every integration step the dihedral feels a pull  
toward it's 180deg opposite position? Or perhaps you want to do this  
(using phiAtTimeZero instead of phi on the right side of the equation):


{ X [ A (1+cos (nT-phi)) ] } - { (1-X)  [ A (1+cos (nT-( phiAtTimeZero  
+ 180 ))) ] }


in place of the equation that you have written (below). In any event,  
if what you are asking is how to slowly change the umbrella then you  
could look into the afm pulling code and see if that is possible for  
dihedrals. Otherwise, you could do what I have suggested previously  
except that you should periodically stop and change the phi value of  
your dihedral restraint in the .top file and then grompp to get the  
updated tpr and then mdrun again. If you are asking how to use a cos  
function and thus be able to use 180deg... then you have me stumped. I  
also tried to do this but I think that it is not currently possible.
If you do use my previous suggestion then please note that there is no  
guarantees that anything you do around a dihedral of about 180 using  
the dihedral restraint will work (since it is not a cos function).  
Therefore you should redefine the value. For example, I am working  
similarly with a chi1 dihedral. For this I have the options of  
N-CA-CB-CG or C'-CA-CB-CG. If I want N-CA-CB-CG to be at 180deg then  
one could instead require that C'-CA-CB-CG be at 60 deg (check this  
actual value for yourself though to ensure that I haven't slipped a  
sign or rotated the wrong direction... this is all from my memory of  
what I set up a while ago).


Please don't hesitate to send another email to the list if you have  
some more questions on this topic.





Quoting Prasad Gajula <[EMAIL PROTECTED]>:


Dear Chris,
Thanks a lot for your answer. I dont know if iam disturbing you. Iam  
 very sorry for that.

Hope you can help me to solve my prolem.
i need to rotate a bond simultaneously from its present orientation   
to opposite orientation.

my idea is like this...
the dihedral angle formula is
[ A (1+cos (nT-phi)) ]  right.
now, i want to do like this...
{ X [ A (1+cos (nT-phi)) ] } - { (1-X)  [ A (1+cos (nT-( phi + 180 ))) ] }
I change the value of X from 1 down to 0, say 0.9, 0.8,.
that means i completely change the orientation of the bond.
Now, my problem is how can i implement this special term in gromacs   
code only for my particular dihedral atoms say B-C (bonded atoms   
A-B-C-D) with simulation continues as usual normally for all other   
bonds.

Please do not mind for sending mail to you personally.

looking forward for your answer.
Thank you very much!
Best regards
Prasad

Message: 9
Date: Wed, 13 Dec 2006 15:54:28 -0500
From: [EMAIL PROTECTED]
Subject: [gmx-users] How to implement dihedral restraints
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"


For example, my peptide is rotating 50 degrees about a bond B-C, out of four
bonded atoms A-B-C-D.  I want to apply additional force on this
dihedral(B-C) during my simulation(only for this particular atoms to make it
rotate further till 180 degrees). All the remaining atoms in the peptide
will have normal force as usual.
May I ask you, how can I apply this in gromacs code.
Any help will be appreciated!


The current manual is good at describing what the options do for
dihedral restraints, but (to my knowlegde) doesn't explain at all how
to get the implementation up and running. Here is how I have done it
based on searching the mailing list for answers. I suggest that
something like this is added by way of example to the manual for
future releases.

Also, the manual is a bit unclear about whether this type of dihedral
restraint is stable for use near 180deg. I have found that for my
system everything appears to behave normally and as expected over the
entire range of dihedral angles including 180deg.

In your .top file:

; Include forcefield parameters
#include "ffoplsaa.itp"
; Include topologies
#include "myprotein.itp"
[ dihedral_restraints ]
; 

Re: [gmx-users] error after genion

2006-12-14 Thread Tsjerk Wassenaar

Hi Carsten,

You've included "ions.itp" twice... Note that this has crossed the
mailing list recently and you could've found the answer by searching
the archive.

Tsjerk

On 12/14/06, Carsten Baldauf <[EMAIL PROTECTED]> wrote:

after i added ions using genion i get this error when i try to run
grompp again:
Generated 165 of the 1596 non-bonded parameter combinations
Cleaning up temporary file grompphYfrXb
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 891

Fatal error:
moleculetype CL- is redefined
---

what am i doing wrong?
cheers//
carsten


--
dr carsten baldauf
biotechnologisches zentrum der tu dresden
http://www.biotec.tu-dresden.de/pisabarro
http://www.biotec.tu-dresden.de/~carstenb

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

No Software Patents!
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Tsjerk A. Wassenaar, Ph.D.
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Biomolecular NMR, Bijvoet Center
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[gmx-users] error after genion

2006-12-14 Thread Carsten Baldauf
after i added ions using genion i get this error when i try to run 
grompp again:

Generated 165 of the 1596 non-bonded parameter combinations
Cleaning up temporary file grompphYfrXb
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 891

Fatal error:
moleculetype CL- is redefined
---

what am i doing wrong?
cheers//
carsten


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dr carsten baldauf
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