Re[2]: 回复： [gmx-users] No such moleculetype Na

[Иимяа Фаамиилиияа]

Change name Cl to name CL and check name Na in forcefield you use (it could be 
NA).


11 декабря 2011, 17:30 от Mark Abraham :
 
  
  
 
 On 11/12/2011 11:43 PM, yp sun wrote:
 The name of ion is different when using different force field You can check 
which field force you use and find out how Na and Cl ion is written in this 
force field.
  
 The molecule name is constant over all force fields in the 4.5 series of 
GROMACS, and the molecule name is all that genion cares about. Atom and residue 
names might vary.
 
 Mark
 

 
 Yeping Sun
 CAS Key Laboratory of Pathogenic Microbiology & Immunology
 INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
 NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
 
 --- 11年12月11日，周日, Setare Jiji  写道：
 
 发件人: Setare Jiji 
 主题: [gmx-users] No such moleculetype Na
 收件人: gmx-users@gromacs.org
 日期: 2011年12月11日,周日,下午5:17
 
 
   
  
   
 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.
 
   
 -下面为附件内容-
 
 
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Re: [gmx-users] No such moleculetype Na

[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: 回复： [gmx-users] No such moleculetype Na

[Mark Abraham]

On 11/12/2011 11:43 PM, yp sun wrote:
The name of ion is different when using different force field You can 
check which field force you use and find out how Na and Cl ion is 
written in this force field.




The molecule name is constant over all force fields in the 4.5 series of 
GROMACS, and the molecule name is all that genion cares about. Atom and 
residue names might vary.


Mark



Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- *11年12月11日，周日, Setare Jiji //* 写道：


发件人: Setare Jiji 
主题: [gmx-users] No such moleculetype Na
收件人: gmx-users@gromacs.org
日期: 2011年12月11日,周日,下午5:17

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.


-下面为附件内容-

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回复： [gmx-users] No such moleculetype Na

[yp sun]

The name of ion is different when using different force field You can check 
which field force you use and find out how Na and Cl ion is written in this 
force field.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- 11年12月11日，周日, Setare Jiji  写道：


发件人: Setare Jiji 
主题: [gmx-users] No such moleculetype Na
收件人: gmx-users@gromacs.org
日期: 2011年12月11日,周日,下午5:17











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.


-下面为附件内容-


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Re: [gmx-users] No such moleculetype Na

[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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[gmx-users] No such moleculetype Na

[Setare Jiji]

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

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

[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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[gmx-users] No such moleculetype Na

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

[YUVRAJ UBOVEJA]

tein 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
> >> <<
> >>
> >> This message and any attachment are intended solely for the addressee
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> >> author of this email do not necessarily reflect the views of the
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> >>
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> >> attachment may still contain software viruses which could damage your
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> >> communications with the University of Nottingham may be monitored as
> >> permitted by UK&  Malaysia legislation.
> >>
> >>   >>
> >>
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell&  Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se<
> http://folding.bmc.uu.se/>
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> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone:  46 18 471 4205  fax: 46 18 511 755
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> -- Forwarded message --
> From: sreelakshmi ramesh 
> To: Discussion list for GROMACS users 
> Date: Sun, 26 Dec 2010 10:58:12 +0530
> Subject: [gmx-users] average pressure too high
> Dear users,
>  I did nvt equil 

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

[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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[gmx-users] No such moleculetype NA+

[shikha agarwal]

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

[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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>
>
>
> --
> 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

[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
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
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>>> www interface or send it to gmx-users-requ...@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
> F: +31-30-2537623
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] No such moleculetype Na

[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
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
> ___
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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

[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
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


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Re: [gmx-users] No such moleculetype Na

[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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[gmx-users] No such moleculetype Na

[swatik]

Hi,
I am performing the simulation of DNA in Gromacs using AMBER03 force
field. The charge on the system is large (-23). I get grompp error when I
add the relevant number of Na+ atoms.

Program grompp_mpi, VERSION 3.3.1
Source code file: toppush.c, line: 1293

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.

Regards,
Swati



-- 
Swati kaushik
Research Scholar
Prof.Sowdhamini's lab
National Centre for Biological Sciences
Tata Institute of Fundamental Research
GKVK,
Bellary Road ,Bangalore,
INDIA

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