[gmx-users] Help on itp and pdb

R R S Pissurlenkar Fri, 06 Sep 2013 11:30:46 -0700

If I use the topology and coordinates of a small molecule from ATB fordocking (structure.pdb / structure.itp which match in atom numbering andsequence); after docking and saving the structure_dock.pdb, the atomnumbering does not match the numbering in the structure.itp file. Thiscauses errors during simulation.How to regular the numbering so that it matches the structure.itp file fromATB


Please help


Regards

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Today's Topics:

  1. Re: Segmentation Fault using g_cluster (deplazes)
  2. Re: Re: Segmentation Fault using g_cluster (Tsjerk Wassenaar)
  3. Re: Segmentation Fault using g_cluster (deplazes)


----------------------------------------------------------------------

Message: 1
Date: Thu, 5 Sep 2013 22:20:16 -0700 (PDT)
From: deplazes <e.depla...@uq.edu.au>
Subject: [gmx-users] Re: Segmentation Fault using g_cluster
To: gmx-users@gromacs.org
Message-ID: <1378444816131-5011007.p...@n6.nabble.com>
Content-Type: text/plain; charset=us-ascii

Hi guys

do you have an idea what is causing the segmentation fault with g_cluster?


I do the following

1 . I combine trr files from different simulations using trjcat and select
backbone atoms only

trjcat  -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc

2. I make a new .tpr file for the backbone atoms only

tpbconv -s run_1.tpr -nsteps -1 -n index.ndx -o topol.tpr

3. I run g_cluster on the combined trajout with the new tpr selecting
backbone for RMSD fit and output

g_cluster -f trajout_combined.xtc -n index.ndx -s topol.tpr -fit -method
gromos -sz clust-size_0.20.xvg -o rmsd-clust_0.20.xpm -g cluster_0.20.log
-clid clust-id_0.20.xvg  -cl clusters_0.20.pdb -dist rmsd-dist_0.20.xvg
-cutoff 0.20

the output is

Allocated 12066120 bytes for frames
Read 1202 frames from trajectory trajout_combined.xtc
Computing 1202x1202 RMS deviation matrix
# RMSD calculations left: 0

The RMSD ranges from 0.0601062 to 0.533457 nm
Average RMSD is 0.321503
Number of structures for matrix 1202
Energy of the matrix is 160.564 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0601062
Making list of neighbors within cutoff 100%
Finding clusters    7

Found 7 clusters

Writing middle structure for each cluster to clusters_0.20.pdb
Segmentation fault


I have tried using less frames (using -dt 500 for trjcat) as to check that
it is not a memory issue but still get the seg fault

The g_cluster works if I use a trajectory from a single simulations but not
for hte combined trajout.

I am getting a segmentation fault with both gromacs 4.5.5 (on my macbook
pro) and 4.6.3 on raijin.nci.org.au (our supercomputing facilities in
Australia)

Cheers
Evelyne



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------------------------------

Message: 2
Date: Fri, 6 Sep 2013 11:10:49 +0200
From: Tsjerk Wassenaar <tsje...@gmail.com>
Subject: Re: [gmx-users] Re: Segmentation Fault using g_cluster
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<cabze1sjhuc9bxcybcrdkeav7bbvbujggcrhvdmvzh7-sghd...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi Evelyne,

I haven't got a clue... But does it work if you use -settime when
concatenating the trajectories, to avoid having frames with the same time
index? It shouldn't cause a segfault, but it might.

Cheers,

Tsjerk

On Fri, Sep 6, 2013 at 7:20 AM, deplazes <e.depla...@uq.edu.au> wrote:

Hi guys

do you have an idea what is causing the segmentation fault with g_cluster?


I do the following

1 . I combine trr files from different simulations using trjcat and select
backbone atoms only

trjcat  -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc

2. I make a new .tpr file for the backbone atoms only

tpbconv -s run_1.tpr -nsteps -1 -n index.ndx -o topol.tpr

3. I run g_cluster on the combined trajout with the new tpr selecting
backbone for RMSD fit and output

g_cluster -f trajout_combined.xtc -n index.ndx -s topol.tpr -fit -method
gromos -sz clust-size_0.20.xvg -o rmsd-clust_0.20.xpm -g cluster_0.20.log
-clid clust-id_0.20.xvg  -cl clusters_0.20.pdb -dist rmsd-dist_0.20.xvg
-cutoff 0.20

the output is

Allocated 12066120 bytes for frames
Read 1202 frames from trajectory trajout_combined.xtc
Computing 1202x1202 RMS deviation matrix
# RMSD calculations left: 0

The RMSD ranges from 0.0601062 to 0.533457 nm
Average RMSD is 0.321503
Number of structures for matrix 1202
Energy of the matrix is 160.564 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0601062
Making list of neighbors within cutoff 100%
Finding clusters    7

Found 7 clusters

Writing middle structure for each cluster to clusters_0.20.pdb
Segmentation fault


I have tried using less frames (using -dt 500 for trjcat) as to check that
it is not a memory issue but still get the seg fault

The g_cluster works if I use a trajectory from a single simulations butnot

for hte combined trajout.

I am getting a segmentation fault with both gromacs 4.5.5 (on my macbook
pro) and 4.6.3 on raijin.nci.org.au (our supercomputing facilities in
Australia)

Cheers
Evelyne



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------------------------------

Message: 3
Date: Fri, 6 Sep 2013 02:50:24 -0700 (PDT)
From: deplazes <e.depla...@uq.edu.au>
Subject: [gmx-users] Re: Segmentation Fault using g_cluster
To: gmx-users@gromacs.org
Message-ID: <ce4fe24f.13be4%e.depla...@uq.edu.au>
Content-Type: text/plain; charset=us-ascii

You're a genious. It works!
Thanks a lot

From: "Tsjerk Wassenaar [via GROMACS]"<ml-node+s5086n5011009...@n6.nabble.com<mailto:ml-node+s5086n5011009...@n6.nabble.com>>

Date: Fri, 6 Sep 2013 02:12:25 -0700
To: Evelyne Deplazes <e.depla...@uq.edu.au<mailto:e.depla...@uq.edu.au>>
Subject: Re: Segmentation Fault using g_cluster

Hi Evelyne,

I haven't got a clue... But does it work if you use -settime when
concatenating the trajectories, to avoid having frames with the same time
index? It shouldn't cause a segfault, but it might.

Cheers,

Tsjerk

On Fri, Sep 6, 2013 at 7:20 AM, deplazes <[hiddenemail]</user/SendEmail.jtp?type=node&node=5011009&i=0>> wrote:

Hi guys

do you have an idea what is causing the segmentation fault with g_cluster?


I do the following

1 . I combine trr files from different simulations using trjcat and select
backbone atoms only

trjcat  -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc

2. I make a new .tpr file for the backbone atoms only

tpbconv -s run_1.tpr -nsteps -1 -n index.ndx -o topol.tpr

3. I run g_cluster on the combined trajout with the new tpr selecting
backbone for RMSD fit and output

g_cluster -f trajout_combined.xtc -n index.ndx -s topol.tpr -fit -method
gromos -sz clust-size_0.20.xvg -o rmsd-clust_0.20.xpm -g cluster_0.20.log
-clid clust-id_0.20.xvg  -cl clusters_0.20.pdb -dist rmsd-dist_0.20.xvg
-cutoff 0.20

the output is

Allocated 12066120 bytes for frames
Read 1202 frames from trajectory trajout_combined.xtc
Computing 1202x1202 RMS deviation matrix
# RMSD calculations left: 0

The RMSD ranges from 0.0601062 to 0.533457 nm
Average RMSD is 0.321503
Number of structures for matrix 1202
Energy of the matrix is 160.564 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0601062
Making list of neighbors within cutoff 100%
Finding clusters    7

Found 7 clusters

Writing middle structure for each cluster to clusters_0.20.pdb
Segmentation fault


I have tried using less frames (using -dt 500 for trjcat) as to check that
it is not a memory issue but still get the seg fault

The g_cluster works if I use a trajectory from a single simulations butnot

for hte combined trajout.

I am getting a segmentation fault with both gromacs 4.5.5 (on my macbook
pro) and 4.6.3 on raijin.nci.org.au (our supercomputing facilities in
Australia)

Cheers
Evelyne



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