from:"Sun Iba"

Re: [gmx-users] mpirun error

2016-10-18 Thread Sun Iba

Thank you very much Andrew

On Wed, Oct 19, 2016 at 10:31 AM, Andrew Guy <andrew@burnet.edu.au>
wrote:

> Hi Sun,
>
> In GROMACS 5.1, all the commands are under the gmx binary. You need to run
> something like:
>
> >> source /your/installation/prefix/here/bin/GMXRC
> >> mpirun -np $NPROCS gmx mdrun_mpi -s md.tpr -c npt.gro -o md_0_1.trr
>
> Go and have a look at some tutorials which use GROMACS 5 or higher, and
> read the manual and documentation. A "No such file or directory" error
> means exactly that - there is no such binary in the gromacs 5.1 directory
> structure.
>
> Andrew
>
> On Wed, Oct 19, 2016 at 3:27 PM, Sun Iba <sun.i...@gmail.com> wrote:
>
> > Dear Gromacs users and experts
> > I am trying to run a test job of 1 ns remotely on supercomputer
> clusters. I
> > have prepared .tpr file in my system (v 5.1.1) and submitted the script
> > file on remote server. following is my script file:
> >
> > ###
> >
> > #!/bin/bash
> > #PBS -l nodes=2:ppn=16
> > #PBS -l walltime=01:00:00
> > #PBS -q TESTq
> > #PBS -e Myerr_$PBS_JOBID
> > #PBS -o myout_$PBS_JOBID
> > #PBS -m abe
> > #PBS -M simranjeetsin...@gmail.com,8725828727
> > #PBS -r n
> > #PBS -V
> > #PBS -A A_B-PR
> >
> >
> > echo PBS JOB id is $PBS_JOBID
> > echo PBS_NODEFILE is $PBS_NODEFILE
> > echo PBS_QUEUE is $PBS_QUEUE
> > NPROCS=`wc -l < $PBS_NODEFILE`
> > NODES=`cat $PBS_NODEFILE | uniq |wc -l`
> > echo NPROCS is $NPROCS
> > echo $PBS_NODEFILE
> >
> >
> >
> > cd /home/external/sggswu/ssingh/test2/
> >
> > source /opt/app/GROMACS/gromacs-5.1.2/env.sh
> >
> > mpirun -np $NPROCS /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi_d -s
> > md.tpr
> > -c npt.gro -o md_0_1.trr
> >
> > 
> > ###
> >
> > AFter execution, the job is terminbated with following error. Please help
> > me resolve it:
> >
> > [proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > [proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
> > (./utils/launch/launch.c:111): execvp error on file
> > /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mpirun error

2016-10-18 Thread Sun Iba

Dear Gromacs users and experts
I am trying to run a test job of 1 ns remotely on supercomputer clusters. I
have prepared .tpr file in my system (v 5.1.1) and submitted the script
file on remote server. following is my script file:

###

#!/bin/bash
#PBS -l nodes=2:ppn=16
#PBS -l walltime=01:00:00
#PBS -q TESTq
#PBS -e Myerr_$PBS_JOBID
#PBS -o myout_$PBS_JOBID
#PBS -m abe
#PBS -M simranjeetsin...@gmail.com,8725828727
#PBS -r n
#PBS -V
#PBS -A A_B-PR


echo PBS JOB id is $PBS_JOBID
echo PBS_NODEFILE is $PBS_NODEFILE
echo PBS_QUEUE is $PBS_QUEUE
NPROCS=`wc -l < $PBS_NODEFILE`
NODES=`cat $PBS_NODEFILE | uniq |wc -l`
echo NPROCS is $NPROCS
echo $PBS_NODEFILE



cd /home/external/sggswu/ssingh/test2/

source /opt/app/GROMACS/gromacs-5.1.2/env.sh

mpirun -np $NPROCS /opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi_d -s md.tpr
-c npt.gro -o md_0_1.trr

###

AFter execution, the job is terminbated with following error. Please help
me resolve it:

[proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
(./utils/launch/launch.c:111): execvp error on file
/opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
[proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
(./utils/launch/launch.c:111): execvp error on file
/opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
[proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
(./utils/launch/launch.c:111): execvp error on file
/opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
[proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
(./utils/launch/launch.c:111): execvp error on file
/opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
[proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
(./utils/launch/launch.c:111): execvp error on file
/opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
[proxy:0:0...@ycn210.en.yuva.param] HYDU_create_process
(./utils/launch/launch.c:111): execvp error on file
/opt/app/GROMACS/gromacs-5.1.2/bin/mdrun_mpi (No such file or directory)
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Catenation of trajectories

2016-10-08 Thread Sun Iba

Hello everyonw


I was wondering if it is possible to catenate multiple trajectories of same
time-step and simulation length into one. Will it over write the
information? For example I have five 50 ns trajectories of protein (time
frames saved at 10 ps interval). The input .pdb file for second 50 ns MD
was extracted from first trajectory and similarly other input files were
extracted from first trajectory. Now I want to catenate these five 50 ns
trajectories into one 250 ns trajectory. Is it possible to catenate these
using gmx trjcat?


Thank you

Suniba
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Small molecule parametrization

2016-09-09 Thread Sun Iba

Justin please have look at PDB coordinates:

HEADERUNCLASSIFIED08-Sep-16
TITLE UNITED ATOM STRUCTURE FOR MOLECULE UNK
AUTHORGROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2016-09-05 10:31:24
AUTHOR   2  http://compbio.biosci.uq.edu.au/atb
HETATM1  C12 SCX10  -1.450  -4.041  -0.077  1.00  0.00   C
HETATM2   O1 SCX10  -2.719  -3.434  -0.134  1.00  0.00   O
HETATM3   C3 SCX10  -2.815  -2.071  -0.157  1.00  0.00   C
HETATM4   C2 SCX10  -4.079  -1.455  -0.012  1.00  0.00   C
HETATM5   C4 SCX10  -1.693  -1.233  -0.290  1.00  0.00   C
HETATM6   H2 SCX10  -0.689  -1.664  -0.419  1.00  0.00   H
HETATM7   C6 SCX10  -5.387  -2.138   0.065  1.00  0.00   C
HETATM8   H4 SCX10  -6.255  -1.451   0.117  1.00  0.00   H
HETATM9   C9 SCX10  -5.767  -3.438   0.069  1.00  0.00   C
HETATM   10  C13 SCX10  -7.246  -3.703   0.131  1.00  0.00   C
HETATM   11   N2 SCX10  -8.455  -3.909   0.168  1.00  0.00   N
HETATM   12  C19 SCX10  -4.965  -4.688   0.013  1.00  0.00   C
HETATM   13   N4 SCX10  -4.368  -5.763  -0.028  1.00  0.00   N
HETATM   14   C1 SCX10  -4.139  -0.046   0.045  1.00  0.00   C
HETATM   15   H1 SCX10  -5.107   0.471   0.159  1.00  0.00   H
HETATM   16   C5 SCX10  -3.004   0.756  -0.044  1.00  0.00   C
HETATM   17   H3 SCX10  -3.100   1.853   0.003  1.00  0.00   H
HETATM   18   C7 SCX10  -1.760   0.161  -0.251  1.00  0.00   C
HETATM   19  C11 SCX10  -0.521   0.988  -0.408  1.00  0.00   C
HETATM   20   H6 SCX10  -0.024   1.023  -1.390  1.00  0.00   H
HETATM   21   N1 SCX10   0.002   1.677   0.531  1.00  0.00   N
HETATM   22   N3 SCX10   1.409   2.643   0.125  1.00  0.00   N
HETATM   23  C16 SCX10   1.077   4.001   0.074  1.00  0.00   C
HETATM   24   O2 SCX10   1.893   4.908   0.253  1.00  0.00   O
HETATM   25  C18 SCX10  -0.392   4.495  -0.144  1.00  0.00   C
HETATM   26   F1 SCX10  -0.916   4.834   1.027  1.00  0.00   F
HETATM   27   F2 SCX10  -0.433   5.577  -0.910  1.00  0.00   F
HETATM   28   F3 SCX10  -1.192   3.601  -0.695  1.00  0.00   F
HETATM   29  C15 SCX10   2.780   2.075   0.077  1.00  0.00   C
HETATM   30  C14 SCX10   3.094   0.702   0.223  1.00  0.00   C
HETATM   31  C10 SCX10   2.068  -0.383   0.443  1.00  0.00   C
HETATM   32  C22 SCX10   4.428   0.269   0.163  1.00  0.00   C
HETATM   33  H11 SCX10   4.661  -0.804   0.260  1.00  0.00   H
HETATM   34  C21 SCX10   5.509   1.132  -0.017  1.00  0.00   C
HETATM   35   C8 SCX10   6.926   0.616  -0.050  1.00  0.00   C
HETATM   36  C20 SCX10   5.211   2.486  -0.157  1.00  0.00   C
HETATM   37  H10 SCX10   6.028   3.213  -0.295  1.00  0.00   H
HETATM   38  C17 SCX10   3.887   2.924  -0.131  1.00  0.00   C
HETATM   39   H8 SCX10   3.778   4.005  -0.281  1.00  0.00   H
CONECT12
CONECT213
CONECT3245
CONECT437   14
CONECT536   18
CONECT65
CONECT7489
CONECT87
CONECT97   10   12
CONECT   109   11
CONECT   11   10
CONECT   129   13
CONECT   13   12
CONECT   144   15   16
CONECT   15   14
CONECT   16   14   17   18
CONECT   17   16
CONECT   185   16   19
CONECT   19   18   20   21
CONECT   20   19
CONECT   21   19   22
CONECT   22   21   23   29
CONECT   23   22   24   25
CONECT   24   23
CONECT   25   23   26   27   28
CONECT   26   25
CONECT   27   25
CONECT   28   25
CONECT   29   22   30   38
CONECT   30   29   31   32
CONECT   31   30
CONECT   32   30   33   34
CONECT   33   32
CONECT   34   32   35   36
CONECT   35   34
CONECT   36   34   37   38
CONECT   37   36
CONECT   38   29   36   39
CONECT   39   38
END



On Fri, Sep 9, 2016 at 5:51 PM, sun.iba2 <sun.i...@gmail.com> wrote:

> This is a small molecule with dicyanovinyl group substituted at para
> position on one of the phenyl ring. I suspect the charges are not proper
> because in ATB the group charges must be -1,0 or 1. For some groups charges
> are summed up to zero but this is not the case of all groups.
>
>
> Sent from Samsung Mobile
>
>
>  Original message 
> From: Justin Lemkul <jalem...@vt.edu>
> Date:09/09/2016 5:18 AM (GMT+05:30)
> To: gmx-us...@gromacs.org
> Cc:
> Subject: Re: [gmx-users] Small molecule parametrization
>
>
>
> On 9/7/16 1:43 PM, Sun Iba wrote:
> > Hi
> > I have parametreized my small m

Re: [gmx-users] Hydrophobic interaction energy

2016-09-07 Thread Sun Iba

How would you define hydrophobic energy? I mean I have heard of hydrophobic
effect that arises due to solvent but this term is new to me. You can
calculate van der Waal term with MM-PBSA etc. People use this energy term
to highlight the role of hydrophobic and non-polar amino acid residues
towards total binding free energy. There are numerous papers in this area.
I don't know how important hydrophobic energy is to you but it seems
difficult to calculate it between protein and ligand particularly. I am not
sure there is a tool.

On Wed, Sep 7, 2016 at 8:22 PM, Nikhil Maroli  wrote:

> For a particular system I wanted to know the hydrophobic energy between the
> ligand and proteins apart from Electro and van der Waals.what is the
> possibility in gromacs? or any other tools available for the same?
>
> --
> Regards,
> Nikhil Maroli
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Small molecule parametrization

2016-09-07 Thread Sun Iba

Hi
I have parametreized my small molecule with the help of ATB server. I have
learnt that ATB provides GROMOS charges better than PRODRG. However, I have
serious doubts regarding the charges assigned to hydrophobic groups. Also I
need to convert the calculated charges into GROMOS 43a1 set (force field I
am using). I am pasting the .itp file produced by ATB:

nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
1   CH31SCX1C1210.223  15.0350
2OE1SCX1 O11   -0.275  15.9994 ; -0.052
3 C1SCX1 C320.476  12.0110
4 C1SCX1 C22   -0.157  12.0110
5 C1SCX1 C42   -0.376  12.0110
6HC1SCX1 H220.172   1.0080 ;  0.115
7 C1SCX1 C630.095  12.0110
8HC1SCX1 H430.137   1.0080
9 C1SCX1 C93   -0.386  12.0110
   10 C1SCX1C1330.478  12.0110
   11NR1SCX1 N23   -0.525  14.0067 ; -0.201
   12 C1SCX1C1940.539  12.0110
   13NR1SCX1 N44   -0.539  14.0067 ;  0.000
   14 C1SCX1 C15   -0.117  12.0110
   15HC1SCX1 H150.157   1.0080
   16 C1SCX1 C55   -0.150  12.0110
   17HC1SCX1 H350.131   1.0080 ;  0.021
   18 C1SCX1 C760.097  12.0110
   19 C1SCX1C1160.247  12.0110
   20HC1SCX1 H660.079   1.0080
   21NR1SCX1 N16   -0.423  14.0067 ;  0.000
   22NT1SCX1 N370.171  14.0067
   23 C1SCX1C1670.387  12.0110
   24 O1SCX1 O27   -0.492  15.9994
   25 C1SCX1C1870.495  12.0110
   26 F1SCX1 F17   -0.187  18.9984
   27 F1SCX1 F27   -0.187  18.9984
   28 F1SCX1 F37   -0.187  18.9984 ;  0.000
   29 C1SCX1C158   -0.211  12.0110
   30 C1SCX1C1480.388  12.0110
   31   CH31SCX1C108   -0.060  15.0350 ;  0.117
   32 C1SCX1C229   -0.444  12.0110
   33HC1SCX1H1190.187   1.0080
   34 C1SCX1C2190.309  12.0110
   35   CH31SCX1 C89   -0.052  15.0350 ;  0.000
   36 C1SCX1C20   10   -0.340  12.0110
   37HC1SCX1H10   100.226   1.0080
   38 C1SCX1C17   10   -0.026  12.0110
   39HC1SCX1 H8   100.140   1.0080 ;  0.000


Please have a look and help me understanding if the charges are too bad.
Also my Nitrogen atom is not aromatic. It is linked to C by triple bond and
to another N by double bond. Does GROMOS treat this type of nitrogn as NT
and NR?

Suniba
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Free energy calculation, Methane in water tutorial

2016-09-03 Thread Sun Iba

The single code from script reproduced the same error:

C































*ommand line:  gmx grompp -f /home/Documents/tutorial/MDP/EM/em_steep.mdp
-c /home/Documents/tutorial/Methane/methane_water.gro -p
/home/Documents/tutorial/Methane/topol.top -o
min.tpr---Program gmx,
VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/futil.cpp, line:
540File input/output error:/home/Documents/tutorial/MDP/EM/em_steep.mdpFor
more information and tips for troubleshooting, please check the
GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
---
GROMACS:  gmx mdrun, VERSION 5.0Executable:
/usr/local/gromacs/bin/gmxLibrary dir:
/usr/local/gromacs/share/gromacs/topCommand line:  mdrun -nt 2 -deffnm
min0Back Off! I just backed up min0.log to
./#min0.log.5#---Program
mdrun, VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line:
513Can not open file:min0.tprFor more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentati *
on/Errors
---


However, I tried using normal command i.e. gmx grompp and dint use the
script and the command worked smoothly. The first minimization step is
complete. I dont know why there is "File input/output" error with script. I
have placed the .mdp files in /home/Docuemnts/tutorial/MDP/EM, as I
mentioned in .sh file:


#!/bin/bash

# Set some environment variables
FREE_ENERGY=/home/Documents/tutorial
echo "Free energy home directory set to $FREE_ENERGY"

MDP=$FREE_ENERGY/MDP/EM
echo ".mdp files are stored in $MDP"

LAMBDA=0

# A new directory will be created for each value of lambda and
# at each step in the workflow for maximum organization.

mkdir Lambda_$LAMBDA
cd Lambda_$LAMBDA

#
# ENERGY MINIMIZATION 1: STEEP  #
#
echo "Starting minimization for lambda = $LAMBDA..."

mkdir EM_1
cd EM_1

# Iterative calls to grompp and mdrun to run the simulations

gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c
$FREE_ENERGY/Methane/methane_water.gro
-p $FREE_ENERGY/Methane/topol.top -o min$LAMBDA.tpr

mdrun -nt 2 -deffnm min$LAMBDA

sleep 10


*Have I messed up with the job.sh?*

On Sat, Sep 3, 2016 at 10:00 AM, sun.iba2  wrote:

> Yes. Doing that. Thank you very much.
>
>
> Sent from Samsung Mobile
>
>
>  Original message 
> From: Nikhil Maroli 
> Date:02/09/2016 7:28 PM (GMT+05:30)
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Cc:
> Subject: Re: [gmx-users] Free energy calculation, Methane in water
> tutorial
>
> run the single code from script and see what prints on the screen,that's
> what Justin suggested
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Free energy calculation, Methane in water tutorial

2016-09-03 Thread Sun Iba

The single code from script reproduced the same error:

C





















































*ommand line:  gmx grompp -f /home/Documents/tutorial/MDP/EM/em_steep.mdp
-c /home/Documents/tutorial/Methane/methane_water.gro -p
/home/Documents/tutorial/Methane/topol.top -o
min.tpr---Program gmx,
VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/futil.cpp, line:
540File input/output error:/home/Documents/tutorial/MDP/EM/em_steep.mdpFor
more information and tips for troubleshooting, please check the
GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
---GROMACS:
gmx mdrun, VERSION 5.0GROMACS is written by:Emile Apol Rossen
Apostolov   Herman J.C. Berendsen Par Bjelkmar   Aldert van Buuren
Rudi van DrunenAnton Feenstra Sebastian Fritsch  Gerrit Groenhof
Christoph Junghans Peter Kasson   Carsten KutznerPer Larsson
Justin A. Lemkul   Magnus LundborgPieter Meulenhoff  Erik Marklund
Teemu Murtola  Szilard Pall   Sander Pronk   Roland Schulz
Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman
Christian Wennberg Maarten Wolf   and the project leaders:Mark Abraham,
Berk Hess, Erik Lindahl, and David van der SpoelCopyright (c) 1991-2000,
University of Groningen, The Netherlands.Copyright (c) 2001-2014, The
GROMACS development team atUppsala University, Stockholm University andthe
Royal Institute of Technology, Sweden.check out http://www.gromacs.org
 for more information.GROMACS is free software; you
can redistribute it and/or modify itunder the terms of the GNU Lesser
General Public Licenseas published by the Free Software Foundation; either
version 2.1of the License, or (at your option) any later
version.GROMACS:  gmx mdrun, VERSION 5.0Executable:
/usr/local/gromacs/bin/gmxLibrary dir:
/usr/local/gromacs/share/gromacs/topCommand line:  mdrun -nt 2 -deffnm
min0Back Off! I just backed up min0.log to
./#min0.log.5#---Program
mdrun, VERSION 5.0Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line:
513Can not open file:min0.tprFor more information and tips for
troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentati *
on/Errors
---


However, I tried using normal command i.e. I dint use the script and the
command worked smoothly. The minimization step is complete. I dont know why
there is "File input/output" error. I have placed the .mdp files in
/home/Docuemnts/tutorial/MDP/EM, as I mentioned in .sh file:


#!/bin/bash

# Set some environment variables
FREE_ENERGY=/home/Documents/tutorial
echo "Free energy home directory set to $FREE_ENERGY"

MDP=$FREE_ENERGY/MDP/EM
echo ".mdp files are stored in $MDP"

LAMBDA=0

# A new directory will be created for each value of lambda and
# at each step in the workflow for maximum organization.

mkdir Lambda_$LAMBDA
cd Lambda_$LAMBDA

#
# ENERGY MINIMIZATION 1: STEEP  #
#
echo "Starting minimization for lambda = $LAMBDA..."

mkdir EM_1
cd EM_1

# Iterative calls to grompp and mdrun to run the simulations

gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c
$FREE_ENERGY/Methane/methane_water.gro -p $FREE_ENERGY/Methane/topol.top -o
min$LAMBDA.tpr

mdrun -nt 2 -deffnm min$LAMBDA

sleep 10


Have I messed up the job.sh?

On Fri, Sep 2, 2016 at 7:28 PM, Nikhil Maroli  wrote:

> run the single code from script and see what prints on the screen,that's
> what Justin suggested
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Free energy calculation, Methane in water tutorial

2016-09-02 Thread Sun Iba

Hello dear users

I am following Justin's tutorial for free energy calculation of Methane in
water. I have downloaded the job.sh file and trying to run it in terminal
using: sh job.sh but it is giving following error:

Program mdrun, VERSION 5.0
Source code file:
/home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513

Can not open file:
min0.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Please help me with error.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] ATB parametrization of small molecule

2016-08-31 Thread Sun Iba

Hello everyone

I want to simulate a protein ligand docked complex using GROMOS96 43a1
force field. I have prepared the ligand topology using ATB server. However,
I want to know how can I validate the results of ATB when no experimental
or computational data is available for small molecule.
I have read in Justin's paper that we can calculate octanol-water partition
coefficient in biphasic system and correlate the logP and other paramteres
with available data. However, in the absence of any experimental or
theoretical proof, is there any way by which I can validate the ATB
parameters? The small molecule contains groups fllowing groups:
N=N, OCH3, Phenyl rings, Cyclohexyl group, -CN, Vinyl group.

Thank you
Suniba
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Time frames missing

2016-08-01 Thread Sun Iba

Hello everyone

I have extended a 100 ns simulation of a protein in water up to 200 ns.
However, the system kept shutting down during the course of simulation and
i had to restart the runs twice. Following are the files I obtained after
completion of mdrun (I am writing information of .xtc only, for .trr its
same:


*md_0_1.xtc = 0 to 100 ns*

*new.xtc = 99.990 to 159.990*

*v.xtc = 166.050 to 179.050*
*traj-comp.xtc = 179.620 to 200.00 ns*

Now I am surprised to see that the time frames from 159.990 to 166.050 are
not written to any file. I have also checked the .trr and .xtc file with
gmx check and found that time frames are incomplete after the follwoing
command:

 gmx check -f new.trr

Checking file new.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time 0.000
# Atoms  133688
Reading frame6000 time 159990.000

*WARNING: Incomplete frame: nr 6607 time 166060*

Item#frames Timestep (ps)
Step  660710
Time  660710
Lambda660710
Coords660710
Velocities660710
Forces   0
Box   660710

Now I am not sure to catenate the avaialble file or should i start the run
again from 159.990 to 166.050? iF YES, WHAT WOULD BE THE COMMAND FOR THAT...

With Regards
Suniba
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Free energy landscpae

2016-07-27 Thread Sun Iba

Hello users and experts
I have performed a protein-ligand simulation with Gromos 43a1 ff and SPC
water model. I performed PCA and selected first 2 principal components for
construction of FEL using gmx sham. However, from the available references
i have seen that the there exist both positive and negative values on FEL
X- and Y-axis around a central 0 value. But in my case, the most populated
region lies far away from 0, i.e. towards "negative" values of PC1
(starting from -2.5 to 0.0; there are no positive values after 0.0) .
Please have a look at this image and suggest why is it so.

https://drive.google.com/drive/my-drive

With Regards
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] FEL - Invitation to view

2016-07-27 Thread Sun Iba (via Google Drive)


I've shared an item with you:

FEL
https://drive.google.com/folderview?id=0Bw28I4GTBqd-cDVyWjRaSVd0Qms=sharing=COKa2skJ=5798ff47

It's not an attachment -- it's stored online. To open this item, just click  
the link above.

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] PCA and gmx analyze

2016-06-27 Thread Sun Iba

Hello Users and experts

My system details:
Force field: GROMOS 43a1

Gromacs version: 5.0

OS: Ubuntu 14.0

Simulation time: 200 ns

No. of eigenvectors and eigenvalues in gmx covar and gmx anaeig: 378
Protein backbone was used for least square fit and covariance analysis. I
am trying to monitor protein folding in the presence of a small molecule
and interested in using first 2 PCs for FEL. Also, I am interested in
assessing if the system is not converged. When I tried to analyze the
cosine content of my eigenvectors with gmx analyze i get following results:

Command line:
  gmx analyze -f proj.xvg -ac autocorr.xvg -msd msd.xvg -cc coscont.xvg -av
average.xvg -ee errest.xvg -b 10 -e 15

Read 1 sets of 5001 points, dt = 10

 std.
dev.  relative deviation of
  standard-
cumulants from those of
set  average deviation  sqrt(n-1)  a
Gaussian distribition

cum. 3   cum. 4
SS1  -2.974823e+00   1.492213e-01   2.110308e-03   0.3810.401



2500, time=25000


*Cosine content of set 1 with 0.5 periods: 1.14745e-05*



Set   1:  err.est. 0.0155418  a 0.693315  tau1 12.3624  tau2 856.505

Back Off! I just backed up autocorr.xvg to ./#autocorr.xvg.1#

Can anyone help me with cosine content of set 1? I dont understand it.
According to manual the cosine content should be closer to 1. Is that value
(* 1.14745e-05) *considered to be closer to 1?
.

Thank You
Suniba
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Hydrophobic interaction analysis

2016-05-13 Thread Sun Iba

hi
Its hydrophobic effect, Nikhil. And you can make index of hydrophobic
groups in your protein, then calculate distance between them.

On Thu, May 12, 2016 at 11:03 PM, Nikhil Maroli  wrote:

> Dear all,
>
> is there any option in gromacs to study the hydrophobic interaction between
> the two molecule over the simulation time !
> --
> Ragards,
> Nikhil Maroli
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Catenation and Visualization

2016-04-22 Thread Sun Iba

Hello Tsjerk
Thank you for your response. I have applied periodic boundary conditions
and have loaded only one file i.e. movie.pdb in Pymol. Thats correct I can
turn visualization off but my question is why two objects are showing up
when I have catenated two trajectories. That's I asked if  used wrong
command for catenation or something is missing. See, I used:

gmx trjcat -f last.xtc latest.xtc -o 100ns.xtc

On Fri, Apr 22, 2016 at 9:05 AM, Tsjerk Wassenaar  wrote:

> Hi Suniba,
>
> For the first part, look up 'periodic boundary conditions' (my oh my, there
> should be a keyboard shortcut for that term). For the second part, it seems
> you have loaded two files, and you should see two objects in the right side
> panel of Pymol. You can turn visualization off by clicking an object.
>
> Hope it helps,
>
> Tsjerk
> On Apr 22, 2016 04:56, "suniba"  wrote:
>
> > Hello everyone
> > I have completed two independent 100 ns simulations of two differnt
> > proteins in water. One is monomer and the other is trimer. Both
> simulations
> > were allowed to run for 50 ns intially, after visulation, trajectories
> were
> > 'correct' and then extended the simulation to 100 ns. Now after
> completion
> > and catenation, when i converted the .xtc into movie.pdb using trjconv,
> the
> > molecule seems broken in all the frames and i am not able to view it in
> > cartoon style. Moreover, when i load the .pdb file of monomer or trimer
> in
> > Pymol, Always two files are getting uploaded. I dont know what is the
> other
> > file but it remains 'static' when i play the movie. Is this visualization
> > problem or i madd a mistake in catenation? Can someone plz give insight
> > With Regards
> >
> > Sent from my iPhone
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

2016-04-07 Thread Sun Iba

The figure is generated using Desmond. Check the following paper:

http://dx.doi.org/10.1016/j.bmc.2014.02.020

On Thu, Mar 31, 2016 at 4:34 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:

> Hi biohpc,
>
> For this you need to combine output from gmx hbond, gmx sasa, and gmx
> saltbr.
>
> Cheers,
>
> Tsjerk
> On Mar 31, 2016 12:58, "bio hpc" <biohpc2...@gmail.com> wrote:
>
> > My problem is not excel or whatever graphical program. I just need the
> > data, in an automatic way. Then I can use either matplotlib or similar to
> > get the plots automatically. But my question is if there is somewhere a
> > repository of gromacs scripts with a script doing an analysis of the
> > protein-ligand itneractions during trajectory. I do not think to be the
> > only one requesting this
> >
> >
> > > El 30/3/2016, a las 6:46, Sun Iba <sun.i...@gmail.com> escribió:
> > >
> > > i am sorry, i replied prior to looking at your figure. Actually, i have
> > > never came across plotting data in this matter. However, I believe you
> > have
> > > tabulated data, so you can use Origin or excel for generating similar
> > > images. You need little effort to arrange the data in desired manner.
> > > Best Wishes
> > >
> > > On Wed, Mar 30, 2016 at 3:15 AM, bio hpc <biohpc2...@gmail.com> wrote:
> > >
> > >> Hi,
> > >>
> > >> after a protein-ligand simulation with gromacs, I would like to be
> able
> > to
> > >> generate a diagram/figure with information about protein-ligand
> > >> interactions, something like this:
> > >>
> > >> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg <
> > >> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg>
> > >>
> > >> I had a look to all gromacs tools but found nothing similar to this.
> > Where
> > >> can I start from?
> > >>
> > >> Thanks,
> > >>
> > >> biohpc
> > >>
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Error: not enough memory

2016-03-22 Thread Sun Iba

Allright
I installed from source. Will do it again.
Thank you very much NIkhil, once again.

On Tue, Mar 22, 2016 at 11:35 AM, Nikhil Maroli  wrote:

> Hi,
> this is problem regarding g_mmpbsa
>
> your not  provided required information such as Gromacs version and
> g_mmpbsa
> installation from source or binary ?!
> in common if you using Gromacs 5.1.1 install g_mmpbsa from binary package
> instead of compiling from source
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Error: not enough memory

2016-03-21 Thread Sun Iba

Dear Gromacs users

I am doing an mm_pbsa analysis of my protein-ligand complex. I installed
and it was nicely running on my workstation Z820. However, on a similar
system, i installed using same steps but it is giving following error:


*Not enough memory. Failed to calloc -1082130432 elements of size 4 for
grps[j].nm_ind(called from file
/home/rajendra/software/gromacs_source/gromacs-5.0.5/src/gromacs/fileio/tpxio.c,
line 2510)*

When i checked the memory of system it is enough i believe:




*sggswu@sggswu:~/Documents/suniba2$ free -m  total
usedfree   shared   buffers cachedMem: 15971
6594   9377 14 66   5401-/+ buffers/cache:
1125  14845Swap:16306  0 16306*

Please help me with error. Is this some gromacs error or shall i post this
problem in mmpbsa mailing forum?

WIth Regards
Suniba
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Extending the simulation

2016-03-07 Thread Sun Iba

Thank you very much.

Regards
Suniba

On Mon, Mar 7, 2016 at 10:09 AM, Nikhil Maroli  wrote:

> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames (sun)

2016-02-04 Thread Sun Iba

Thank You very much :)

Regards
Suniba

On Fri, Feb 5, 2016 at 4:00 AM, Björn Sommer 
wrote:

> Hello Everyone
>> I have performed a md simulation if protein in water for 10ns and frames
>> were obtained after every 10ps. I wanted to visualize the.gro and
>> trajectory file in VMD, without water, so I prepared an index file
>> containing protein only. Using editcon i removed water from md.gro as well
>> but I loaded the files in VMD, 1000 time frames are loaded but I cannot see
>> any change in structure or per frame conformation. The protein is still. I
>> am not clear what to do. I tried keeping water in .trr and then in .gro and
>> repeated steps but no results. When I use original .trr and .gro, only then
>> i visualize the change in structure. Please help me
>>
>> Regards
>> Suniba
>>
> Hi Suniba,
>
> sorry, but this is not the way how you should use VMD! It is much more
> comfortable.
>
> You first import the PDB file, then you import the TRR or XTC file (make
> sure that the actual PDB file is selected during loading, so that the
> trajectory is associated with it). You may also first make the following
> settings after importing the PDB, and then afterwards import the
> trajectory. This might save time during loading and memory resources.
>
> Okay, you open now the representations window (Graphics ->
> Representations).
>
> In the Representations window, select the tab "Selections". In the keyword
> section, select "resname". Now, you will see in the field value all Residue
> IDs contained in your PDB file. Use this IDs now in the selection.
>
> For example, water has often the name SOL or WAT etc. If you want to see
> only the water, type in into the "Selected Atoms" section
>
> resname SOL
>
> If you want to see everything else, not the water, and also not the ions,
> which could have the name NA, you say
>
> not resname SOL NA
>
> You want to see only the P atoms of DPPE with the resname DPE
>
> (resname DPE) and (name P8')
>
> Please note that, to select single molecules, you should have a look to
> the original PDB file and check what the names of the atoms for the
> corresponding molecule look like.
>
> To change now the representations, you find all options in the "Draw
> stlye" tab.
>
> Now you want to have different representations for different atoms: just
> click on "Create Rep". The last representation is duplicated, and you can
> change it now. By double clicking on the entry in the list, you can hidea
> an entry.
>
> Have fun!
> Bjorn
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Atom type SDMSO not found

2015-07-28 Thread Sun Iba

Here is the generated topology of ligand with PRODRG server, i believe
something is wrong with atom typs here;

 PRODRG COORDS
   29
1UNK  CLAW 1   1.328  -0.638  -0.151
1UNK  CAM  2   1.384  -0.765  -0.049
1UNK  SAU  3   1.520  -0.861  -0.089
1UNK  CAG  4   1.503  -0.954   0.053
1UNK  CLAV 5   1.606  -1.085   0.095
1UNK  CAN  6   1.396  -0.913   0.128
1UNK  HAR  7   1.368  -0.958   0.223
1UNK  CAO  8   1.327  -0.803   0.069
1UNK  SAT  9   1.181  -0.728   0.145
1UNK  OAR 10   1.144  -0.805   0.261
1UNK  OAS 11   1.215  -0.589   0.171
1UNK  NAQ 12   1.058  -0.732   0.029
1UNK  HAS 13   1.052  -0.655  -0.035
1UNK  CAC 14   0.963  -0.835   0.018
1UNK  CAD 15   0.837  -0.802  -0.035
1UNK  HAD 16   0.817  -0.699  -0.065
1UNK  CAE 17   0.739  -0.899  -0.051
1UNK  HAE 18   0.642  -0.870  -0.093
1UNK  CAB 19   0.987  -0.969   0.051
1UNK  HAB 20   1.085  -0.998   0.090
1UNK  CAA 21   0.887  -1.065   0.036
1UNK  HAA 22   0.908  -1.168   0.066
1UNK  CAF 23   0.759  -1.034  -0.015
1UNK  NAP 24   0.657  -1.133  -0.031
1UNK  CAH 25   0.519  -1.090  -0.064
1UNK  CAI 26   0.421  -1.196  -0.011
1UNK  CAJ 27   0.447  -1.336  -0.069
1UNK  CAK 28   0.595  -1.359  -0.104
1UNK  CAL 29   0.690  -1.276  -0.016
   1.33540   1.33540   1.33540

The atom types look strange to me. Please help

On Wed, Jul 29, 2015 at 10:18 AM, su sun.i...@gmail.com wrote:

 Hello everyone
 I am doing protein-ligand simulation according to Justin's tutorial. After
 running gmx grompp command, i encountered following error:
 Fatal error:
 Atomtype SDMSO not found.
 Is this the force field matching problem? because i am not able to find
 out any such atom types in any of the generated files.
 Please guide me where the problem is. All other commands ran properly.

 Suniba
 Sent from my iPhone
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] LINCS WARNING

2015-07-14 Thread Sun Iba

Hello Everyone
I am simulation a protein as per the lysozyme tutorial. MY simulation got
dumped at final mdrun step. It is showing following warning :

Command line:
  gmx mdrun -deffnm md_0_1

Reading file md_0_1.tpr, VERSION 5.0.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
starting mdrun 'AMYLOID BETA A4 PROTEIN'
50 steps,   2500.0 ps.

Step 166, time 0.83 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000162, max 0.000714 (between atoms 158 and 159)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
628629   30.00.1090   0.1090  0.1090

Step 170, time 0.85 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000234, max 0.005085 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
623624   73.10.1090   0.1084  0.1090
628629   55.10.1090   0.1089  0.1090

Step 171, time 0.855 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023399, max 1.013176 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
623624   89.90.1084   0.2194  0.1090
Wrote pdb files with previous and current coordinates

Step 172, time 0.86 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000453, max 0.015917 (between atoms 628 and 629)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
623624   44.80.2194   0.1084  0.1090
628629   75.50.1093   0.1073  0.1090

Step 173, time 0.865 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.639970, max 23.410875 (between atoms 628 and 629)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
619621   30.30.1339   0.1284  0.1335
621622   46.90.1013   0.1019  0.1010
623624   89.70.1084   1.7118  0.1090
623625   72.50.1530   0.2719  0.1529
623638   43.10.1525   0.1587  0.1522
625626   46.90.1091   0.1372  0.1090
625627   61.50.1093   0.1643  0.1090
625628   89.30.1530   0.3458  0.1529
628629   90.00.1073   2.6608  0.1090
628630   74.10.1531   0.2413  0.1529
628634   88.30.1530   0.2401  0.1529
634635   41.20.1091   0.1433  0.1090
634636   38.20.1091   0.1357  0.1090
634637   39.00.1091   0.1380  0.1090
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 623 and 629
at distance 2.823 which is larger than the table limit 2.042 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



Step 174, time 0.87 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.212190, max 85.046806 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
260263   90.00.1090   0.3693  0.1090
621622   70.20.1019   0.1815  0.1010
621623   41.50.1556   0.2046  0.1449
623624   90.51.7119   9.3791  0.1090
623625  126.50.2719   0.4357  0.1529
623638   62.10.1587   0.1499  0.1522
625626   96.20.1372   3.6085  0.1090
625627  115.30.1643   0.8026  0.1090
625628  115.40.3458   1.3529  0.1529
628630  125.40.2413   0.8808  0.1529
628634  147.00.2401   0.6961  0.1529
630633  134.30.0801   0.0868  0.1090
634635  118.30.1433   0.3006  0.1090
634636   77.60.1357   0.2433  0.1090
634637   56.30.1380   0.1960  0.1090
638640   33.70.1388   0.0773  0.1335
Wrote pdb files with previous and current coordinates

Step 175, time 0.875 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 14884.476208, max 642183.562500 (between atoms 634 and 636)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
227229   30.30.1090   0.1118  0.1090
234236   90.00.1090   1.5776  0.1090
249250   89.90.1090   0.4785  0.1090

Re: [gmx-users] mpirun error

[gmx-users] mpirun error

[gmx-users] Catenation of trajectories

Re: [gmx-users] Small molecule parametrization

Re: [gmx-users] Hydrophobic interaction energy

[gmx-users] Small molecule parametrization

Re: [gmx-users] Free energy calculation, Methane in water tutorial

Re: [gmx-users] Free energy calculation, Methane in water tutorial

[gmx-users] Free energy calculation, Methane in water tutorial

[gmx-users] ATB parametrization of small molecule

[gmx-users] Time frames missing

[gmx-users] Free energy landscpae

[gmx-users] FEL - Invitation to view

[gmx-users] PCA and gmx analyze

Re: [gmx-users] Hydrophobic interaction analysis

Re: [gmx-users] Catenation and Visualization

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

Re: [gmx-users] Error: not enough memory

[gmx-users] Error: not enough memory

Re: [gmx-users] Extending the simulation

Re: [gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames (sun)

Re: [gmx-users] Atom type SDMSO not found

[gmx-users] LINCS WARNING

23 matches

Site Navigation

Mail list logo

Footer information