Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Timo Graen

On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:

Hi GMX Users, please help me
I am trying to begin a simulation of a protein and ligand coplex by 
gromacs4.6.3.

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 (solv.gro, 102546)
does not match topology (topol.top, 133916)

whe i use tip3p, i don't get error.

Thank you very much


Use share/gromacs/top/tip4p.gro when generating the simulation box, 
tip4p has an aditional interaction site


best
timo

--
--
T.M.D. Graen
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department, 105 00
Am Fassberg 11
37077 Goettingen, Germany
Tel.:  ++49 551 201 2313
Fax:  ++49 551 201 2302
Email: tgr...@gwdg.de
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Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mahboobeh Eslami
dear timo
Please send me further details. I'm not a professional.
Thanks and regards




On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote:
 
On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:

 Hi GMX Users, please help me
 I am trying to begin a simulation of a protein and ligand coplex by 
 gromacs4.6.3.

 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 (solv.gro, 102546)
 does not match topology (topol.top, 133916)

 whe i use tip3p, i don't get error.

 Thank you very much

Use share/gromacs/top/tip4p.gro when generating the simulation box, 
tip4p has an aditional interaction site

best
timo

--
--
T.M.D. Graen
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department, 105 00
Am Fassberg 11
37077 Goettingen, Germany
Tel.:  ++49 551 201 2313
Fax:  ++49 551 201 2302
Email: tgr...@gwdg.de
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Maybe you should modify your .tpr file manually according to what you added
in the previous sections!




On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami 
mahboobeh.esl...@yahoo.com wrote:

 dear timo
 Please send me further details. I'm not a professional.
 Thanks and regards




 On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote:

 On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:

  Hi GMX Users, please help me
  I am trying to begin a simulation of a protein and ligand coplex by
 gromacs4.6.3.
 
  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 (solv.gro, 102546)
  does not match topology (topol.top, 133916)
 
  whe i use tip3p, i don't get error.
 
  Thank you very much

 Use share/gromacs/top/tip4p.gro when generating the simulation box,
 tip4p has an aditional interaction site

 best
 timo

 --
 --
 T.M.D. Graen
 Max Planck Institute for Biophysical Chemistry
 Theoretical and Computational Biophysics Department, 105 00
 Am Fassberg 11
 37077 Goettingen, Germany
 Tel.:  ++49 551 201 2313
 Fax:  ++49 551 201 2302
 Email: tgr...@gwdg.de
 --
 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

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 send a mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Justin Lemkul



On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote:

Maybe you should modify your .tpr file manually according to what you added
in the previous sections!



Manually modify a .tpr?  How would one do that?

The OP needs to provide the exact commands issued.  The fatal error shown 
results from poor bookkeeping (i.e. not making use of the -p option of genbox 
and genion) or use of the wrong water coordinate file.


I would also suggest some basic tutorial material to become more familiar with 
simple Gromacs tasks.


-Justin





On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami 
mahboobeh.esl...@yahoo.com wrote:


dear timo
Please send me further details. I'm not a professional.
Thanks and regards




On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de wrote:

On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:


Hi GMX Users, please help me
I am trying to begin a simulation of a protein and ligand coplex by

gromacs4.6.3.


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 (solv.gro, 102546)
does not match topology (topol.top, 133916)

whe i use tip3p, i don't get error.

Thank you very much


Use share/gromacs/top/tip4p.gro when generating the simulation box,
tip4p has an aditional interaction site

best
timo

--
--
T.M.D. Graen
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department, 105 00
Am Fassberg 11
37077 Goettingen, Germany
Tel.:  ++49 551 201 2313
Fax:  ++49 551 201 2302
Email: tgr...@gwdg.de
--
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-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Oh, I am sorry, I made a big mistake! :)

Best Regards


On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote:

 Maybe you should modify your .tpr file manually according to what you
 added
 in the previous sections!


 Manually modify a .tpr?  How would one do that?

 The OP needs to provide the exact commands issued.  The fatal error shown
 results from poor bookkeeping (i.e. not making use of the -p option of
 genbox and genion) or use of the wrong water coordinate file.

 I would also suggest some basic tutorial material to become more familiar
 with simple Gromacs tasks.

 -Justin





 On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami 
 mahboobeh.esl...@yahoo.com wrote:

  dear timo
 Please send me further details. I'm not a professional.
 Thanks and regards




 On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de
 wrote:

 On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:

  Hi GMX Users, please help me
 I am trying to begin a simulation of a protein and ligand coplex by

 gromacs4.6.3.


 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 (solv.gro, 102546)
 does not match topology (topol.top, 133916)

 whe i use tip3p, i don't get error.

 Thank you very much


 Use share/gromacs/top/tip4p.gro when generating the simulation box,
 tip4p has an aditional interaction site

 best
 timo

 --
 --
 T.M.D. Graen
 Max Planck Institute for Biophysical Chemistry
 Theoretical and Computational Biophysics Department, 105 00
 Am Fassberg 11
 37077 Goettingen, Germany
 Tel.:  ++49 551 201 2313
 Fax:  ++49 551 201 2302
 Email: tgr...@gwdg.de
 --
 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-requ...@gromacs.org.


 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 ==

 --
 Gromacs Users mailing list

 * Please search the archive at http://www.gromacs.org/
 Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Mohsen Ramezanpour
Dear Justin
I meant modifying  .top  file after adding some ions and water molecules
which could be equivalent to -p option as you mentioned.
What do you think about this?
Please let me know



On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour 
ramezanpour.moh...@gmail.com wrote:

 Oh, I am sorry, I made a big mistake! :)

 Best Regards


 On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote:

 Maybe you should modify your .tpr file manually according to what you
 added
 in the previous sections!


 Manually modify a .tpr?  How would one do that?

 The OP needs to provide the exact commands issued.  The fatal error shown
 results from poor bookkeeping (i.e. not making use of the -p option of
 genbox and genion) or use of the wrong water coordinate file.

 I would also suggest some basic tutorial material to become more familiar
 with simple Gromacs tasks.

 -Justin





 On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami 
 mahboobeh.esl...@yahoo.com wrote:

  dear timo
 Please send me further details. I'm not a professional.
 Thanks and regards




 On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de
 wrote:

 On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:

  Hi GMX Users, please help me
 I am trying to begin a simulation of a protein and ligand coplex by

 gromacs4.6.3.


 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 (solv.gro, 102546)
 does not match topology (topol.top, 133916)

 whe i use tip3p, i don't get error.

 Thank you very much


 Use share/gromacs/top/tip4p.gro when generating the simulation box,
 tip4p has an aditional interaction site

 best
 timo

 --
 --
 T.M.D. Graen
 Max Planck Institute for Biophysical Chemistry
 Theoretical and Computational Biophysics Department, 105 00
 Am Fassberg 11
 37077 Goettingen, Germany
 Tel.:  ++49 551 201 2313
 Fax:  ++49 551 201 2302
 Email: tgr...@gwdg.de
 --
 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-requ...@gromacs.org.


 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 ==

 --
 Gromacs Users mailing list

 * Please search the archive at http://www.gromacs.org/
 Support/Mailing_Lists/GMX-Users_List before posting!

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 send a mail to gmx-users-requ...@gromacs.org.



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Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Justin Lemkul



On 11/28/13 10:13 AM, Mohsen Ramezanpour wrote:

Dear Justin
I meant modifying  .top  file after adding some ions and water molecules
which could be equivalent to -p option as you mentioned.
What do you think about this?


That would be one possible solution, but it is not yet clear what the OP has 
done or failed to do correctly.  One does not need to make manual modifications 
if -p has properly been used with genbox and genion.  The fact that the 
coordinate file specifies fewer atoms than the topology suggests that perhaps 
the wrong water coordinates were used (e.g. a 3-point model instead of a 4-point 
model), as would happen if one follows tutorials too literally and specifies 
genbox -cs spc216.gro instead of -cs tip4p.gro.


Many things could be wrong.  The OP needs to provide more details so we can stop 
guessing and arrive at a solution.


-Justin


Please let me know



On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour 
ramezanpour.moh...@gmail.com wrote:


Oh, I am sorry, I made a big mistake! :)

Best Regards


On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote:




On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote:


Maybe you should modify your .tpr file manually according to what you
added
in the previous sections!



Manually modify a .tpr?  How would one do that?

The OP needs to provide the exact commands issued.  The fatal error shown
results from poor bookkeeping (i.e. not making use of the -p option of
genbox and genion) or use of the wrong water coordinate file.

I would also suggest some basic tutorial material to become more familiar
with simple Gromacs tasks.

-Justin






On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami 
mahboobeh.esl...@yahoo.com wrote:

  dear timo

Please send me further details. I'm not a professional.
Thanks and regards




On Thursday, November 28, 2013 4:28 PM, Timo Graen tgr...@gwdg.de
wrote:

On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote:

  Hi GMX Users, please help me

I am trying to begin a simulation of a protein and ligand coplex by


gromacs4.6.3.



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 (solv.gro, 102546)
does not match topology (topol.top, 133916)

whe i use tip3p, i don't get error.

Thank you very much



Use share/gromacs/top/tip4p.gro when generating the simulation box,
tip4p has an aditional interaction site

best
timo

--
--
T.M.D. Graen
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department, 105 00
Am Fassberg 11
37077 Goettingen, Germany
Tel.:  ++49 551 201 2313
Fax:  ++49 551 201 2302
Email: tgr...@gwdg.de
--
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-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==

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Support/Mailing_Lists/GMX-Users_List before posting!

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send a mail to gmx-users-requ...@gromacs.org.






--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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