[gmx-users] Re: segentation fault -core dumped
Keerthana S.P Periasamy
keerthanasp33 at yahoo.com
Sat Sep 22 08:10:12 CEST 2012
Hi
I want to simulate a metalloprotein which contains Zn metal ion. I getting am error in the equillibration part as
wrote pdb coordinates with current and previous coordinates
segmentation fault (core dumped)
--- On Sat, 9/22/12, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:
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Subject: gmx-users Digest, Vol 101, Issue 77
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Date: Saturday, September 22, 2012, 4:35 AM
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Today's Topics:
1. Re: Gromos force fields and simulation of the alpha-helices
membrane proteins (Justin Lemkul)
2. Re: Water molecule can not be settled - mdrun error
(Justin Lemkul)
3. Re: Water molecule can not be settled - mdrun error (Peter C. Lai)
4. Re: TIP4P water model (Peter C. Lai)
5. Re: TIP4P water model (Justin Lemkul)
6. About Presence of Bond In Topology (vidhya sankar)
----------------------------------------------------------------------
Message: 1
Date: Fri, 21 Sep 2012 14:43:24 -0400
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Gromos force fields and simulation of the
alpha-helices membrane proteins
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <505CB54C.7090303 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 9/21/12 2:33 PM, James Starlight wrote:
> Dear Gromacs Users!
>
> In some recent publications about protein dynamics investigation I've
> found reference about new gromos force field (56A7) where some fix in
> case of dihedral terms have been included.
>
> During my simulation performed with the 56A6 ff I've noticed that in
> some cases short alpha helices fragments were unfolded during 50-100ns
> of simulation. In particular that was in cases of simulation of
> membrane receptors. In some of that proteins I've observed unfolding
> of the part of the alpha helices which were placed in the water layer
> ( the rest of the alpha helices embedded in the membrane layer was
> very stable during all simulation time ). So I wounder to know if that
> events were the artifacts of the 56A6 force field or there are some
> biological-significance of such dynamics seen in the water layer.
> Is it possible to obtain new 56A7 ff and integrate it into Gromacs (
> I'm using version 4.54). ?
>
54A7 force field files can be obtained from ATB:
http://compbio.biosci.uq.edu.au/atb/
> Will the systems (topologies) made for 56A6 ff compatible with the
> 56A7 ff ( In particular I'm using Berger's lipids) or should I create
> my protein-in-membrane system again ?
>
If you're using a different force field, you have to recreate the topologies.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 2
Date: Fri, 21 Sep 2012 14:59:17 -0400
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Water molecule can not be settled - mdrun
error
To: Lara Bunte <lara.bunte at yahoo.de>, Discussion list for GROMACS
users <gmx-users at gromacs.org>
Message-ID: <505CB905.6080005 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 9/21/12 1:31 PM, Lara Bunte wrote:
> Hi Justin
>
> I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with this settings grompp gives me two notes and one of this notes is inconsistent:
>
> NOTE 1 [file pr.mdp]:
> For energy conservation with switch/shift potentials, rlist should be 0.1
> to 0.3 nm larger than rvdw.
>
> Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my CHARMM27 force field.
>
>
Increase rlist as suggested to accommodate the algorithm. Since CHARMM does not
use charge groups (well, it uses single-atom charge groups) this isn't such a
big deal. For a force field like Gromos96, it matters a lot more.
>
> My second note is:
>
> NOTE 2 [file pr.mdp]:
> The sum of the two largest charge group radii (0.079505) is larger than
> rlist (1.200000) - rvdw (1.200000)
>
>
> which I sadly don't understand.
>
http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 3
Date: Fri, 21 Sep 2012 15:13:58 -0500
From: "Peter C. Lai" <pcl at uab.edu>
Subject: Re: [gmx-users] Water molecule can not be settled - mdrun
error
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <20120921201357.GM94109 at cesium.hyperfine.info>
Content-Type: text/plain; charset="us-ascii"
On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
>
>
> On 9/21/12 1:31 PM, Lara Bunte wrote:
> > Hi Justin
> >
> > I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with this settings grompp gives me two notes and one of this notes is inconsistent:
> >
> > NOTE 1 [file pr.mdp]:
> > For energy conservation with switch/shift potentials, rlist should be 0.1
> > to 0.3 nm larger than rvdw.
> >
> > Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my CHARMM27 force field.
> >
> >
>
> Increase rlist as suggested to accommodate the algorithm. Since CHARMM does not
> use charge groups (well, it uses single-atom charge groups) this isn't such a
> big deal. For a force field like Gromos96, it matters a lot more.
Actually rlist has to be equal to rvdw for this case (PME will complain if it
doesn't). I haven't had a water settling issue in a correctly setup system
with rlist = rvdw and a switched rvdw. I do remember a bug in the code that
forgets rlistlong is specified.
>
> >
> > My second note is:
> >
> > NOTE 2 [file pr.mdp]:
> > The sum of the two largest charge group radii (0.079505) is larger than
> > rlist (1.200000) - rvdw (1.200000)
> >
> >
> > which I sadly don't understand.
> >
>
> http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>
> -Justin
>
I also get this note too, but the sum looks fine to me. If the sum > 0.15 then
it typically indicates chargegroups are being used, which they shouldn't for
charmm-based forcefields, but in this case the distance shown is on the order
of a heavy-h bond. I think the note message is still related to rlist vs.
rlistlong.
anyway, I routinely ignore both these notes and it hasn't given me problems
so far. I would still go bck to check the specific water that could not settle
and see what the other particles near it are since that is probably the root
of the problem. Also, we haven't been told what the results of the energy
minimzation was...
--
==================================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
==================================================================
------------------------------
Message: 4
Date: Fri, 21 Sep 2012 18:55:24 -0500
From: "Peter C. Lai" <pcl at uab.edu>
Subject: Re: [gmx-users] TIP4P water model
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <20120921235524.GO2559 at uab.hyperfine.info>
Content-Type: text/plain; charset="us-ascii"
Perhaps genion is not removing the dummy atoms properly?
On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote:
> Hi all,
>
> I am trying to begin a simulation of a protein.
>
> I am using AMBER99sb-ILDN force field and TIP4P water model. However,
> I am facing a problem in the ion adding step.
>
> when I issue the grompp command to generate the necessary .tpr file
> for simulation to be utilised by genion tool, I get the following
> error :
>
> "Fatal error:
> number of coordinates in coordinate file (system_solv.gro, 421880)
> does not match topology (topol.top, 416008)
> "
>
> However, I have rechecked several times my topology file and the
> co-ordinate file and I am running it pretty straightforward to get
> this error. When I try TIP3P water model for the same protein, I do
> not get the error.
>
> I get the same error when I use TIP4P-Ew water model too. I have
> decide a better water model for my system before I run my final
> production simulations and so I have been trying to compare both the
> water models. I am wondering if anyone could kindly suggest the
> possible reason for this error because ideally, it should not be
> giving me any error at this stage as I haven't manipulated with
> anything.
>
> I am also appending my ions.mdp info below:
>
> ; ions.mdp - used as input into grompp to generate ions.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
> emstep = 0.01 ; Energy step size
> nsteps = 50000 ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how
> to calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and long range forces
> ns_type = grid ; Method to determine neighbor list (simple, grid)
> rlist = 0.9 ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME ; Treatment of long range electrostatic interactions
> rcoulomb = 0.9 ; Short-range electrostatic cut-off
> rvdw = 0.9 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>
> -----------
>
>
>
> --
> Ankita Naithani
> --
> 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!
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--
==================================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
==================================================================
------------------------------
Message: 5
Date: Fri, 21 Sep 2012 19:57:38 -0400
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] TIP4P water model
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <505CFEF2.1020109 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 9/21/12 7:55 PM, Peter C. Lai wrote:
> Perhaps genion is not removing the dummy atoms properly?
>
The problem is occurring with grompp before genion. We would need to see all
the prior commands (exactly copied and pasted from the terminal) as well as the
[molecules] section of the topology, to at least start to guess at what's wrong.
It is unusual to find a failure in grompp before genion.
-Justin
> On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote:
>> Hi all,
>>
>> I am trying to begin a simulation of a protein.
>>
>> I am using AMBER99sb-ILDN force field and TIP4P water model. However,
>> I am facing a problem in the ion adding step.
>>
>> when I issue the grompp command to generate the necessary .tpr file
>> for simulation to be utilised by genion tool, I get the following
>> error :
>>
>> "Fatal error:
>> number of coordinates in coordinate file (system_solv.gro, 421880)
>> does not match topology (topol.top, 416008)
>> "
>>
>> However, I have rechecked several times my topology file and the
>> co-ordinate file and I am running it pretty straightforward to get
>> this error. When I try TIP3P water model for the same protein, I do
>> not get the error.
>>
>> I get the same error when I use TIP4P-Ew water model too. I have
>> decide a better water model for my system before I run my final
>> production simulations and so I have been trying to compare both the
>> water models. I am wondering if anyone could kindly suggest the
>> possible reason for this error because ideally, it should not be
>> giving me any error at this stage as I haven't manipulated with
>> anything.
>>
>> I am also appending my ions.mdp info below:
>>
>> ; ions.mdp - used as input into grompp to generate ions.tpr
>> ; Parameters describing what to do, when to stop and what to save
>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>> emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
>> emstep = 0.01 ; Energy step size
>> nsteps = 50000 ; Maximum number of (minimization) steps to perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how
>> to calculate the interactions
>> nstlist = 1 ; Frequency to update the neighbor list and long range forces
>> ns_type = grid ; Method to determine neighbor list (simple, grid)
>> rlist = 0.9 ; Cut-off for making neighbor list (short range forces)
>> coulombtype = PME ; Treatment of long range electrostatic interactions
>> rcoulomb = 0.9 ; Short-range electrostatic cut-off
>> rvdw = 0.9 ; Short-range Van der Waals cut-off
>> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>>
>> -----------
>>
>>
>>
>> --
>> Ankita Naithani
>> --
>> 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
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 6
Date: Sat, 22 Sep 2012 12:33:31 +0800 (SGT)
From: vidhya sankar <scvsankar_agr at yahoo.com>
Subject: [gmx-users] About Presence of Bond In Topology
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<1348288411.4333.YahooMailNeo at web193105.mail.sg3.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Dear Justin Thank you for your Reply
After pdb2gmx When i Visualize the resultant .gro file of my cyclic peptide in VMD
I have Observed the Bond Between Nitrogen atom (N ) of First residue and Carbon atom (C) of Last residue I have not observed The same bond when I open and Visualize in Chimera . Then How Could i Confirm Whether the bond is present or Not?
Thanks in Advance
------------------------------
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