[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 74
Yaser Hosseini
yaser.hosseini.biologist at gmail.com
Wed Dec 17 09:21:12 CET 2014
hi
thank you for your replay dear justin
after that error i can solve it with your help i got one more fatal error
in nvt step , i do every thing that you said in your tutorial but i cant
pass this step:
mdrun deffnm nvt
error:
starting mdrun 'Protein in water'
50000 steps, 100.0 ps.
step 0
Step 14, time 0.028 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009678, max 0.394560 (between atoms 5800 and 5799)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5800 5799 87.7 0.1140 0.1590 0.1140
5801 5800 57.0 0.1430 0.1569 0.1430
Step 15, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 17.388239, max 723.890869 (between atoms 5800 and 5799)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5814 5813 123.4 0.1090 0.4470 0.1090
5821 5813 127.8 0.1390 0.3625 0.1390
5816 5815 119.8 0.1730 0.3944 0.1730
5817 5815 115.3 0.1390 0.4924 0.1390
5818 5817 44.3 0.1090 0.1780 0.1090
5819 5817 40.7 0.1390 0.2064 0.1390
5822 5821 31.6 0.1360 0.1742 0.1360
5800 5799 89.1 0.1590 82.6376 0.1140
5801 5800 102.1 0.1569 36.6296 0.1430
5802 5801 88.8 0.1561 18.1129 0.1390
5804 5801 115.7 0.1591 31.4161 0.1390
5803 5802 135.3 0.1154 10.3695 0.1090
5810 5802 95.1 0.1466 4.9405 0.1390
5805 5804 34.3 0.1135 6.6124 0.1090
5806 5804 93.7 0.1436 8.7402 0.1390
5807 5806 105.7 0.1746 4.8713 0.1730
5808 5806 155.0 0.1410 2.0440 0.1390
5809 5808 125.3 0.1100 2.4187 0.1090
5810 5808 144.1 0.1410 3.8807 0.1390
5811 5810 132.3 0.1376 7.3234 0.1360
5812 5811 106.9 0.1364 7.5677 0.1360
5813 5812 98.9 0.1391 1.2296 0.1390
5815 5812 98.8 0.1391 1.3506 0.1390
Wrote pdb files with previous and current coordinates
WARNING: Listed nonbonded interaction between particles 5799 and 5802
at distance 3f which is larger than the table limit 3f 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.
-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/pme.c, line: 851
Fatal error:
1 particles communicated to PME node 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension
x.This usually means that your system is not well equilibrated.
what can i do ??
thank you.
On Wed, Dec 17, 2014 at 7:56 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. fatal erroe in prorein-ligand comlex (Yaser Hosseini)
> 2. Re: fatal erroe in prorein-ligand comlex (Justin Lemkul)
> 3. Re: fatal erroe in prorein-ligand comlex (Justin Lemkul)
> 4. Re: fatal erroe in prorein-ligand comlex (Bikash Ranjan Sahoo)
> 5. Re: fatal erroe in prorein-ligand comlex (Justin Lemkul)
> 6. Re: Ions drifting (jani vinod)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 17 Dec 2014 01:52:32 +0330
> From: Yaser Hosseini <yaser.hosseini.biologist at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: [gmx-users] fatal erroe in prorein-ligand comlex
> Message-ID:
> <CAPK_XJTacJ9wpA3SthBuYh8zSA2tr0n6=
> JMNk_s6uKQRuiJ_sA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> hi gromacs users
>
> i got error in step four in protein-ligand complex how can i fix it:
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 144131)
> does not match topology (topol.top, 144171)
>
> when i want to ran this:
>
> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>
> i add my ligand drg.gro in protein_processed.gro.
>
> beside i cant find conf.gro that you say in this toturial:
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html
>
> thank you .
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 16 Dec 2014 21:05:36 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] fatal erroe in prorein-ligand comlex
> Message-ID: <5490E4F0.2000604 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/16/14 5:22 PM, Yaser Hosseini wrote:
> > hi gromacs users
> >
> > i got error in step four in protein-ligand complex how can i fix it:
> >
> > Fatal error:
> > number of coordinates in coordinate file (solv.gro, 144131)
> > does not match topology (topol.top, 144171)
> >
> > when i want to ran this:
> >
> > grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
> >
> > i add my ligand drg.gro in protein_processed.gro.
> >
> > beside i cant find conf.gro that you say in this toturial:
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html
> >
>
> conf.gro is the default output name from pdb2gmx; it's just a typo in the
> tutorial.
>
> The solution to your problem is always the same - proper bookkeeping. Your
> topology specifies something that is not in the coordinate file (the
> ligand,
> perhaps?) that has 40 atoms.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 16 Dec 2014 21:07:33 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] fatal erroe in prorein-ligand comlex
> Message-ID: <5490E565.20607 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/16/14 9:05 PM, Justin Lemkul wrote:
> >
> >
> > On 12/16/14 5:22 PM, Yaser Hosseini wrote:
> >> hi gromacs users
> >>
> >> i got error in step four in protein-ligand complex how can i fix it:
> >>
> >> Fatal error:
> >> number of coordinates in coordinate file (solv.gro, 144131)
> >> does not match topology (topol.top, 144171)
> >>
> >> when i want to ran this:
> >>
> >> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
> >>
> >> i add my ligand drg.gro in protein_processed.gro.
> >>
> >> beside i cant find conf.gro that you say in this toturial:
> >>
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html
> >>
> >>
> >
> > conf.gro is the default output name from pdb2gmx; it's just a typo in
> the tutorial.
> >
>
> Actually, it's not a typo:
>
> Copy 3HTB_processed.gro to a new file to be manipulated, for instance,
> call it
> "conf.gro."
>
> It's just a safety measure in case you mess something up; you haven't
> wrecked
> the actual pdb2gmx output. Perhaps I should call it something different to
> avoid clashes with default names. Apparently I had even confused myself
> before
> I checked...
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 17 Dec 2014 11:11:48 +0900
> From: Bikash Ranjan Sahoo <bikash.bioinformatic at protein.osaka-u.ac.jp>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] fatal erroe in prorein-ligand comlex
> Message-ID:
> <CAK1Bc4nz_AW9fFZ1cetwzJBophXuEd0bmN1XPmpsWc=
> J02ObKA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Yaser,
> Gro file is sensitive and you should update the number manually after
> adding the ligand atoms to the protein.gro file. Check the first line of
> your protein.gro and ligand.gro. In the complex.gro the first line should
> be the summation of both. Gromacs does not perform it manually. Kindly chck
> again and rerun the grompp.
>
>
> Good luck
> Bikash
> Osaka
>
> On Wednesday, December 17, 2014, Yaser Hosseini <
> yaser.hosseini.biologist at gmail.com> wrote:
>
> > hi gromacs users
> >
> > i got error in step four in protein-ligand complex how can i fix it:
> >
> > Fatal error:
> > number of coordinates in coordinate file (solv.gro, 144131)
> > does not match topology (topol.top, 144171)
> >
> > when i want to ran this:
> >
> > grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
> >
> > i add my ligand drg.gro in protein_processed.gro.
> >
> > beside i cant find conf.gro that you say in this toturial:
> >
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html
> >
> > thank you .
> > --
> > 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-request at gromacs.org <javascript:;>.
> >
>
>
> --
> Warm regards
> Bikash Ranjan Sahoo
> Sent from I Phone 5
> Osaka, Japan
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 16 Dec 2014 21:15:42 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] fatal erroe in prorein-ligand comlex
> Message-ID: <5490E74E.70505 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/16/14 9:11 PM, Bikash Ranjan Sahoo wrote:
> > Dear Yaser,
> > Gro file is sensitive and you should update the number manually after
> > adding the ligand atoms to the protein.gro file. Check the first line of
> > your protein.gro and ligand.gro. In the complex.gro the first line should
> > be the summation of both. Gromacs does not perform it manually. Kindly
> chck
> > again and rerun the grompp.
> >
>
> Incorrect formatting or contents of the .gro file should not trigger this
> fatal
> error; there are other error messages if there are too many or too few
> atoms in
> the .gro file.
>
> -Justin
>
> >
> > Good luck
> > Bikash
> > Osaka
> >
> > On Wednesday, December 17, 2014, Yaser Hosseini <
> > yaser.hosseini.biologist at gmail.com> wrote:
> >
> >> hi gromacs users
> >>
> >> i got error in step four in protein-ligand complex how can i fix it:
> >>
> >> Fatal error:
> >> number of coordinates in coordinate file (solv.gro, 144131)
> >> does not match topology (topol.top, 144171)
> >>
> >> when i want to ran this:
> >>
> >> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
> >>
> >> i add my ligand drg.gro in protein_processed.gro.
> >>
> >> beside i cant find conf.gro that you say in this toturial:
> >>
> >>
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html
> >>
> >> thank you .
> >> --
> >> 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-request at gromacs.org <javascript:;>.
> >>
> >
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 17 Dec 2014 09:55:59 +0530
> From: jani vinod <genomejani at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Ions drifting
> Message-ID:
> <CABp6ott3zVscez59whNXEiYdEKvmX+h7SeDhXroXy5=
> GX_5_2Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Justin,
> Thanks for reply
> I am using following attached mdp file
> In raw trajectory protein molecule appears to be broken but ions around it
> . So I processed the trajectory with trjconv whole option followed by
> nojump.
> After that the protein appear on one side and ions on other
>
> Thanks
> Vinod
>
>
>
> On Tue, Dec 16, 2014 at 6:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> >
> > On 12/16/14 1:34 AM, jani vinod wrote:
> >
> >> Dear All,
> >> I am trying to carry out simulation of protein at 0.5 mM concentration
> of
> >> NaCl.
> >> It has been observed that within few nanosecond ions begin to drift in
> one
> >> direction and protein in other direction. I am using Amberff03 force
> >> filed.
> >> What may the reason for the same.
> >>
> >>
> > No idea unless you show us your .mdp file and any commands you're giving.
> > Is this drift observed in the raw trajectory, or in something you've
> > manipulated with trjconv?
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > 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-request at 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
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> send a mail to gmx-users-request at gromacs.org.
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>
> End of gromacs.org_gmx-users Digest, Vol 128, Issue 74
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