[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 74

Abid Channa abid_channa04 at yahoo.com
Wed Dec 17 06:51:06 CET 2014


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, 36526)
            does not match topology (topol.top, 365267)

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.
Thanks,,

Regards,,

Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research,International Center for Chemical and
Biological Sciences,University of Karachi-75270.Karachi-Pakistan.
UAN #(92-21) 111-222-292 Ext. (309)
Cell # +923013553051
      From: "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se>
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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.
>

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

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