Re: [gmx-users] No such moleculetype Na

2011-12-11 Thread m_p 

Did you try NA or CL.
All caps worked for me last time I used this.
Egy


On Dec 11, 2011, at 4:17 AM, Setare Jiji wrote:



Hi,
Thanks for your responding.

I checked my ions.itp file in which file sodium and chlorine ions  
are as Na and Cl form.


Thus, I used genion as follows:

genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn  
8 -pname Na


Unfortunately, I encountered same fatal error.

any help will highly appreciated.

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Re: [gmx-users] No such moleculetype Na

2011-12-11 Thread Mark Abraham 

On 11/12/2011 8:17 PM, Setare Jiji wrote:

Hi,
Thanks for your responding.

I checked my ions.itp file in which file sodium and chlorine ions are 
as Na and Cl form.


Thus, I used genion as follows:

genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 
-pname Na


Unfortunately, I encountered same fatal error.



Then you were either not looking at the right file, or not looking at 
the right name. As genion -h says, you need to use the molecule name, 
not the atom name or residue name.


Mark
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Re: [gmx-users] No such moleculetype Na

2011-12-10 Thread cuong nguyen 
Hi Setare,

You should find the ions.itp file in your computer, open and see the exact
name of sodium in this file. Use this name when using the command "genion".

Good luck!

Cuong

2011/12/10 Setare Jiji 

>   Hi,
>
> I am running Tutorial 1: Lysozyme in 
> Water
> .
> I used 4-0-7 version and the sequence is true but in minimization energy
> step,I have this fatal error:
>   No such moleculetype Na
> so,what do I do?
>
> Best regards
>
>
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Mobile: (+61) 452213981
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Re: [gmx-users] No such moleculetype Na

2011-12-10 Thread Tsjerk Wassenaar 
Hi Setare,

That tutorial is made for later gromacs versions, as stated at the
beginning. The naming of ions has changed since 4.0.*.

Cheers,

Tsjerk

On Dec 10, 2011 1:00 PM, "Setare Jiji"  wrote:

Hi,

I am running Tutorial 1: Lysozyme in
Water
.
I used 4-0-7 version and the sequence is true but in minimization energy
step,I have this fatal error:
  No such moleculetype Na
so,what do I do?

Best regards


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Re: [gmx-users] No such moleculetype NA+

2010-12-26 Thread YUVRAJ UBOVEJA 
Hello Shikha

Replace NA+ with NA in your topol.top file.
It will solve the problem as it recognise NA for NA+.

Thanks

Yuvraj
IIIT Hyderabad

On Sun, Dec 26, 2010 at 12:26 PM,  wrote:

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>   1. Re: Replicating an experiment (David van der Spoel)
>   2. RE: Replicating an experiment (NG HUI WEN)
>   3. average pressure too high (sreelakshmi ramesh)
>   4. No such moleculetype NA+ (shikha agarwal)
>
>
> -- Forwarded message --
> From: David van der Spoel 
> To: Discussion list for GROMACS users 
> Date: Sat, 25 Dec 2010 22:55:34 +0100
> Subject: Re: [gmx-users] Replicating an experiment
> On 12/25/10 6:37 PM, NG HUI WEN wrote:
>
>> Thank you David for your prompt and useful reply :)  I am in fact
>> simulating a membrane protein.
>>
>> It's good to know I can use the "generate-new-starting-velocity" method.
>> But, do you mind to elaborate a bit more what you mean by "if you simulate
>> long enough"?
>>
>> I would like to try your suggestion of picking a random structure from an
>> elevated temperature simulation. Can I achieve that by taking my existing
>> membrane protein system,
>> 1) pass it through grompp with a new mdp (with higher temperature) to
>> produce a new .tpr file
>> 2) simulate the system for a period (perhaps 1 ns)
>> 3) take any frame / final structure
>> 4) pass it through grompp again (with original mdp with temperature 300K,
>> gen_seed = -1) to produce the .tpr file for my replicate?
>>
>>  Yes that is what I meant. Of course you should check that your protein is
> not unfolding, or you membrane going into the wrong phase.
>
>  Thanks very much indeed!!
>>
>> 
>>
>> From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel
>> Sent: Sat 12/25/2010 10:28 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Replicating an experiment
>>
>>
>>
>> On 2010-12-25 15.05, NG HUI WEN wrote:
>>
>>> Dear all,
>>> Merry Xmas! I have a very quick question here which i'd like to pick
>>> your brain on, would really appreciate a reply.
>>> I am planning to replicate an experiment that I have carried out. Just
>>> wondering what is the best way to do it? I am thinking of changing the
>>> starting velocity of my system by setting a random number e.g 23412445
>>> etc in the gen_seed section as below, not sure if it is meaningful to do
>>> so?
>>> gen_vel = yes
>>> gen_temp = 300.0
>>> gen_seed = random number
>>> Thank you for your input!
>>>
>> That will work fine, if you simulate long enough. Consider that the
>> starting structure may also influence how different your results  will
>> be, e.g. for a protein in water. For liquids there is no such problem.
>> You can do a simulation and slightly elevated temperature and pick
>> structures from that with a different random seed, in order to randomize
>> your simulations even more.
>>
>>> HW
>>> <<
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>> --
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Re: [gmx-users] No such moleculetype NA+

2010-12-25 Thread John Wesly . J 
Have a look at the rtp file of the force field u r using for correct
representation of the ion used..

With regards,
 J. John Wesly,
 FInal Year, B.Tech., Bioinformatics,
 School of Chemical and Biotechnology,
 SASTRA University, Thanjavur,
 Tamil Nadu, India.

<~WesFaith~>
"He who desire to learn, pursues towards edification... One who has will to
do, finds a way how to do.
  Have a LEARNING SPREE Desire to learn... Passion to know things...
Unravel the mysteries about your abilities... "


On Sun, Dec 26, 2010 at 12:26 PM, shikha agarwal wrote:

> hello ,
>
> this is my ions.itp file for gromos53a6 forcefield
>
> [ moleculetype ]
> ; molnamenrexcl
> CU11
>
> [ atoms ]
> ; idat typeres nr residu nameat name  cg nrcharge
> mass
> 1CU1+1CU1CU 11 63.54600
>
> [ moleculetype ]
> ; molnamenrexcl
> CU1
>
> [ atoms ]
> ; idat typeres nr residu nameat name  cg nrcharge
> mass
> 1CU2+1CUCU 12 63.54600
>
> [ moleculetype ]
> ; molnamenrexcl
> ZN1
>
> [ atoms ]
> ; idat typeres nr residu nameat name  cg nrcharge
> mass
> 1ZN2+1ZNZN 12 65.37000
> this  is my ions.itp
>
> [ moleculetype ]
> ; molnamenrexcl
> MG1
>
> [ atoms ]
> ; idat typeres nr residu nameat name  cg nrcharge
> mass
> 1MG2+1MGMG 12 24.30500
>
> [ moleculetype ]
> ; molnamenrexcl
> CA1
>
> [ atoms ]
> ; idat typeres nr residu nameat name  cg nrcharge
> mass
> 1CA2+1CACA 12 40.08000
>
> [ moleculetype ]
> ; molnamenrexcl
> NA1
>
> [ atoms ]
> ; idat typeres nr residu nameat name  cg nrcharge
> mass
> 1NA+1NANA 11 22.9898
>
> [ moleculetype ]
> ; molnamenrexcl
> CL1
>
> [ atoms ]
> ; idat typeres nr residu nameat name  cg nrcharge
> mass
> 1CL-1CLCL 1-1 35.45300
>
>
>
>
> for adding ions I used this command ...
>
> genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11
> -nname CL-
>
> now when I m doing EM then getting this error
>
> grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr
>
> Fatal error:
> No such moleculetype NA+
>
>
> help me !
>
> regards:
> shikha
>
>
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Re: [gmx-users] No such moleculetype Na

2009-04-22 Thread swatik 
Hi Tsjerk,

Thanks for your suggestions.After including molecule types from ions.itp
for OPLS force field,its working fine now.

Thanks again.
Regards,
Swati


> Hi Swati,
>
> Sorry, I wasn't  paying that much attention indeed and failed to
> notice you were dealing with Amber. There's nothing wrong with your
> installation in this regard; Gromacs just does not have Amber included
> by default. I'm not sure if there's an ions.itp for Amber somewhere,
> but it's not too hard writing the moleculetype 'Na' yourself. Just
> take one of the ones in ions.itp and set the names and atom type
> accordingly.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Apr 22, 2009 at 10:14 AM,   wrote:
>> Hi Tsjerk,
>> Thanks for your reply. ions.itp is already included in topology file.
>> However after you mentioned I checked the ions.itp file. But I think it
>> defines molecule type only for gromacs force fields and the OPLS force
>> field. The headers are only these three
>> #ifdef _FF_GROMACS
>> #ifdef _FF_GROMOS96
>> #ifdef _FF_OPLS
>> Is this a problem with my GROMACS installation? Kindly advice.
>> Thanks.
>> Swati
>>
>>
>>> Hi Swati,
>>>
 Fatal error:
 No such moleculetype Na

 But the atom type is present in ffamber03.rtp. I tried changing the
 atom
 name to NA and Na+. But I still get similar error. Kindly help.
>>>
>>> It doesn't complain about the atom type, but about the moleculetype.
>>> Did you #include "ions.itp"? That file contains the moleculetype
>>> definitions for a series of ions, including Na/NA/NA+. The naming
>>> depends on the force field.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>> Junior UD (post-doc)
>>> Biomolecular NMR, Bijvoet Center
>>> Utrecht University
>>> Padualaan 8
>>> 3584 CH Utrecht
>>> The Netherlands
>>> P: +31-30-2539931
>>> F: +31-30-2537623
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
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>>
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
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Re: [gmx-users] No such moleculetype Na

2009-04-22 Thread swatik 
Hi Tsjerk,
 Thanks for your suggestion.I tried to change the ions.itp as follows :

#ifdef _FF_AMBER03

[ moleculetype ]
; molname   nrexcl
Na+ 1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge
1   Na  1   Na  Na   1  1

#endif

But still I am getting same problem.Kindly advice.

Regards,
Swati


> Hi Swati,
>
> Sorry, I wasn't  paying that much attention indeed and failed to
> notice you were dealing with Amber. There's nothing wrong with your
> installation in this regard; Gromacs just does not have Amber included
> by default. I'm not sure if there's an ions.itp for Amber somewhere,
> but it's not too hard writing the moleculetype 'Na' yourself. Just
> take one of the ones in ions.itp and set the names and atom type
> accordingly.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Apr 22, 2009 at 10:14 AM,   wrote:
>> Hi Tsjerk,
>> Thanks for your reply. ions.itp is already included in topology file.
>> However after you mentioned I checked the ions.itp file. But I think it
>> defines molecule type only for gromacs force fields and the OPLS force
>> field. The headers are only these three
>> #ifdef _FF_GROMACS
>> #ifdef _FF_GROMOS96
>> #ifdef _FF_OPLS
>> Is this a problem with my GROMACS installation? Kindly advice.
>> Thanks.
>> Swati
>>
>>
>>> Hi Swati,
>>>
 Fatal error:
 No such moleculetype Na

 But the atom type is present in ffamber03.rtp. I tried changing the
 atom
 name to NA and Na+. But I still get similar error. Kindly help.
>>>
>>> It doesn't complain about the atom type, but about the moleculetype.
>>> Did you #include "ions.itp"? That file contains the moleculetype
>>> definitions for a series of ions, including Na/NA/NA+. The naming
>>> depends on the force field.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>> Junior UD (post-doc)
>>> Biomolecular NMR, Bijvoet Center
>>> Utrecht University
>>> Padualaan 8
>>> 3584 CH Utrecht
>>> The Netherlands
>>> P: +31-30-2539931
>>> F: +31-30-2537623
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>>
>>
>> ___
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> ___
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Re: [gmx-users] No such moleculetype Na

2009-04-22 Thread Tsjerk Wassenaar 
Hi Swati,

Sorry, I wasn't  paying that much attention indeed and failed to
notice you were dealing with Amber. There's nothing wrong with your
installation in this regard; Gromacs just does not have Amber included
by default. I'm not sure if there's an ions.itp for Amber somewhere,
but it's not too hard writing the moleculetype 'Na' yourself. Just
take one of the ones in ions.itp and set the names and atom type
accordingly.

Hope it helps,

Tsjerk

On Wed, Apr 22, 2009 at 10:14 AM,   wrote:
> Hi Tsjerk,
> Thanks for your reply. ions.itp is already included in topology file.
> However after you mentioned I checked the ions.itp file. But I think it
> defines molecule type only for gromacs force fields and the OPLS force
> field. The headers are only these three
> #ifdef _FF_GROMACS
> #ifdef _FF_GROMOS96
> #ifdef _FF_OPLS
> Is this a problem with my GROMACS installation? Kindly advice.
> Thanks.
> Swati
>
>
>> Hi Swati,
>>
>>> Fatal error:
>>> No such moleculetype Na
>>>
>>> But the atom type is present in ffamber03.rtp. I tried changing the atom
>>> name to NA and Na+. But I still get similar error. Kindly help.
>>
>> It doesn't complain about the atom type, but about the moleculetype.
>> Did you #include "ions.itp"? That file contains the moleculetype
>> definitions for a series of ions, including Na/NA/NA+. The naming
>> depends on the force field.
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>> ___
>> gmx-users mailing list    gmx-us...@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] No such moleculetype Na

2009-04-22 Thread swatik 
Hi Tsjerk,
Thanks for your reply. ions.itp is already included in topology file.
However after you mentioned I checked the ions.itp file. But I think it
defines molecule type only for gromacs force fields and the OPLS force
field. The headers are only these three
#ifdef _FF_GROMACS
#ifdef _FF_GROMOS96
#ifdef _FF_OPLS
Is this a problem with my GROMACS installation? Kindly advice.
Thanks.
Swati


> Hi Swati,
>
>> Fatal error:
>> No such moleculetype Na
>>
>> But the atom type is present in ffamber03.rtp. I tried changing the atom
>> name to NA and Na+. But I still get similar error. Kindly help.
>
> It doesn't complain about the atom type, but about the moleculetype.
> Did you #include "ions.itp"? That file contains the moleculetype
> definitions for a series of ions, including Na/NA/NA+. The naming
> depends on the force field.
>
> Cheers,
>
> Tsjerk
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> ___
> gmx-users mailing listgmx-users@gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] No such moleculetype Na

2009-04-22 Thread Tsjerk Wassenaar 
Hi Swati,

> Fatal error:
> No such moleculetype Na
>
> But the atom type is present in ffamber03.rtp. I tried changing the atom
> name to NA and Na+. But I still get similar error. Kindly help.

It doesn't complain about the atom type, but about the moleculetype.
Did you #include "ions.itp"? That file contains the moleculetype
definitions for a series of ions, including Na/NA/NA+. The naming
depends on the force field.

Cheers,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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