[gmx-users] Help on itp and pdb
R R S Pissurlenkar
raghuvir at bcpindia.org
Fri Sep 6 20:29:34 CEST 2013
If I use the topology and coordinates of a small molecule from ATB for
docking (structure.pdb / structure.itp which match in atom numbering and
sequence); after docking and saving the structure_dock.pdb, the atom
numbering does not match the numbering in the structure.itp file. This
causes errors during simulation.
How to regular the numbering so that it matches the structure.itp file from
ATB
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.deplazes at uq.edu.au>
Subject: [gmx-users] Re: Segmentation Fault using g_cluster
To: gmx-users at gromacs.org
Message-ID: <1378444816131-5011007.post at 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 <tsjerkw at gmail.com>
Subject: Re: [gmx-users] Re: Segmentation Fault using g_cluster
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CABzE1SjhuC9bxcYBcrDKEav7BBVbUjggCrHVdMVzH7-sGhdtng at 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.deplazes at 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 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
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Segmentation-Fault-using-g-cluster-tp4662864p5011007.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Tsjerk A. Wassenaar, Ph.D.
------------------------------
Message: 3
Date: Fri, 6 Sep 2013 02:50:24 -0700 (PDT)
From: deplazes <e.deplazes at uq.edu.au>
Subject: [gmx-users] Re: Segmentation Fault using g_cluster
To: gmx-users at gromacs.org
Message-ID: <CE4FE24F.13BE4%e.deplazes at 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+s5086n5011009h79 at n6.nabble.com<mailto:ml-node+s5086n5011009h79 at n6.nabble.com>>
Date: Fri, 6 Sep 2013 02:12:25 -0700
To: Evelyne Deplazes <e.deplazes at uq.edu.au<mailto:e.deplazes at 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 <[hidden
email]</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 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
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Segmentation-Fault-using-g-cluster-tp4662864p5011007.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list [hidden
> email]</user/SendEmail.jtp?type=node&node=5011009&i=1>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [hidden
> email]</user/SendEmail.jtp?type=node&node=5011009&i=2>.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Tsjerk A. Wassenaar, Ph.D.
--
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