Re: [gmx-users] Error in grompp minimization

[Souilem Safa]

Dear Justin,
thank you for your reply.
Yes, you are right , I have corrected it already and now it works well.
Cheers,
Safa


On 11 June 2013 09:53, Justin Lemkul  wrote:

>
>
> On 6/10/13 8:51 PM, Souilem Safa wrote:
>
>> Dear gromacs users,
>>
>> I'm trying to simulate a single molecule in cyclohexane.
>> I made a box of my molecule using editconf command and next I solvate with
>> cyclohexane using genbox command :
>> genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro
>>
>> I did next a position restraint in the topolgy file and I tried to
>> minimize, i got this fatal error:
>> Fatal error:
>> No such moleculetype CHX
>>
>> What could be the origin of this error.
>>
>
> You probably forgot to #include the topology that introduces CHX as a
> valid [moleculetype].
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] Error in grompp minimization

[Justin Lemkul]

On 6/10/13 8:51 PM, Souilem Safa wrote:

Dear gromacs users,

I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro

I did next a position restraint in the topolgy file and I tried to
minimize, i got this fatal error:
Fatal error:
No such moleculetype CHX

What could be the origin of this error.


You probably forgot to #include the topology that introduces CHX as a valid 
[moleculetype].


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Error in grompp minimization

[Souilem Safa]

Dear gromacs users,

I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro

I did next a position restraint in the topolgy file and I tried to
minimize, i got this fatal error:
Fatal error:
No such moleculetype CHX

What could be the origin of this error.
Thanks :)
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Re: [gmx-users] error in grompp

[Justin Lemkul]

On 10/7/12 8:42 PM, Nur Syafiqah Abdul Ghani wrote:

Dear All,

Fatal error:
number of coordinates in coordinate file (prot_wtr_solv.gro, 18031)
  does not match topology (control.top, 16650)

It happen when i started to minimize it by using the command

grompp -v -f minim_first.mdp -p control.top -c prot_wtr_solv.gro -o
minim_prot.tpr -zero

When i open the control.top and the prot_wtr_solv.gro file and i
startet to calculate the missing atom is about 1381 which is for my
DRG molecule..
I already edit and put the topology like below :

; Include topology for DRG
#include "solvent.itp"

[ system ]
; Name
ALZHEIMER'S DISEASE AMYLOID in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
DRG1381
SOL   350

Can you guys please explain it to me why this happened..Its still cant
be minimize it yet..



The answer to this error is always the same.

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

You need to keep better track of the molecules in your system and adjust the 
topology accordingly.  When dealing with complex systems, you must do your own 
bookkeeping.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] error in grompp

[Justin Lemkul]

On 10/2/12 11:26 AM, Shine A wrote:

Sir,

 I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But grompp (before minimization of system_inflated.gro) giving error like
this..
Fatal error:
Atomtype LC3 not found

Actually what changes I should do on the system topology, before grompp?
  I found that atomtype LC3 is found in my dppc.itp file.



If you're following my tutorial, then you have skipped a step or not completed 
the force field modifications.  Go back and ensure that ffnonbonded.itp has been 
modified correctly to include the atom types and parameters from lipid.itp.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] error in grompp

[Shine A]

Sir,

I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But grompp (before minimization of system_inflated.gro) giving error like
this..
Fatal error:
Atomtype LC3 not found

Actually what changes I should do on the system topology, before grompp?
 I found that atomtype LC3 is found in my dppc.itp file.
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Re: [gmx-users] error in grompp

[reisingere]

Hi Justin,
thank you very much for your help!!

>
>
> On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi Justin,
>> thank you for your answer.
>>
>> Now I tried it with two different restraint .itp files. One for the
>> protein and one for the dummy atoms.
>> But still it doesn't work. Now the error is:
>>
>> [ file posre_memb.itp, line 5 ]:
>> Atom index (4942) in position_restraints out of bounds (1-1).
>> This probably means that you have inserted topology section
>> "position_restraints"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "position_restraints" section to the right
>> molecule.
>>
>>
>> But I think I included it the right way:
>>
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Include water topology
>> #include "amber03.ff/tip3p.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>> 11   1000   1000   1000
>> #endif
>>
>> ; Include topology for ions
>> #include "amber03.ff/ions.itp"
>>
>> #include "amber03.ff/dum.itp"
>> #ifdef POSRES
>> #include "posre_memb.itp"
>> #endif
>>
>>
>>
>> In my coordiate file the difference between them look like this:
>>
>> 313LEU   HD23 4938   3.813   4.505   3.308
>>313LEU  C 4939   3.435   4.335   3.190
>>313LEUOC1 4940   3.429   4.330   3.090
>>313LEUOC2 4941   3.337   4.305   3.259
>>314DUMDUM 4942   1.996   2.371   6.171
>>314DUMDUM 4943   1.996   2.371   6.271
>>314DUMDUM 4944   1.996   2.471   6.171
>>314DUMDUM 4945   1.996   2.471   6.271
>>
>>
>> my restraint file for the protein looks like this:
>>
>>
>> ; position restraints for Protein-H of GROup of MAchos and Cynical
>> Suckers
>>
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>> 11   1000   1000   1000
>> 41   1000   1000   1000
>> 71   1000   1000   1000
>>101   1000   1000   1000
>>131   1000   1000   1000
>>
>>
>> and my restraint file for the dummy atoms look like this:
>>
>> ; position restraints for Protein-H of GROup of MAchos and Cynical
>> Suckers
>>
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>> 49421   1000   1000   1000
>> 49431   1000   1000   1000
>> 49441   1000   1000   1000
>> 49451   1000   1000   1000
>>
>>
>> What is wrong?
>>
>
> Atom numbering is done per [moleculetype] and has nothing to do with the
> atom
> numbers in the coordinate file.  If you have a one-atom dummy
> [moleculetype],
> then the only valid content of posre_memb.itp is:
>
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
> 11   1000   1000   1000
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
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Re: [gmx-users] error in grompp

[Justin A. Lemkul]

On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi Justin,
thank you for your answer.

Now I tried it with two different restraint .itp files. One for the
protein and one for the dummy atoms.
But still it doesn't work. Now the error is:

[ file posre_memb.itp, line 5 ]:
Atom index (4942) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


But I think I included it the right way:


; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "amber03.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

; Include topology for ions
#include "amber03.ff/ions.itp"

#include "amber03.ff/dum.itp"
#ifdef POSRES
#include "posre_memb.itp"
#endif



In my coordiate file the difference between them look like this:

313LEU   HD23 4938   3.813   4.505   3.308
   313LEU  C 4939   3.435   4.335   3.190
   313LEUOC1 4940   3.429   4.330   3.090
   313LEUOC2 4941   3.337   4.305   3.259
   314DUMDUM 4942   1.996   2.371   6.171
   314DUMDUM 4943   1.996   2.371   6.271
   314DUMDUM 4944   1.996   2.471   6.171
   314DUMDUM 4945   1.996   2.471   6.271


my restraint file for the protein looks like this:


; position restraints for Protein-H of GROup of MAchos and Cynical Suckers

[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
41   1000   1000   1000
71   1000   1000   1000
   101   1000   1000   1000
   131   1000   1000   1000


and my restraint file for the dummy atoms look like this:

; position restraints for Protein-H of GROup of MAchos and Cynical Suckers

[ position_restraints ]
;  i funct   fcxfcyfcz
49421   1000   1000   1000
49431   1000   1000   1000
49441   1000   1000   1000
49451   1000   1000   1000


What is wrong?



Atom numbering is done per [moleculetype] and has nothing to do with the atom 
numbers in the coordinate file.  If you have a one-atom dummy [moleculetype], 
then the only valid content of posre_memb.itp is:


[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] error in grompp

[reisingere]

Hi Justin,
thank you for your answer.

Now I tried it with two different restraint .itp files. One for the
protein and one for the dummy atoms.
But still it doesn't work. Now the error is:

[ file posre_memb.itp, line 5 ]:
Atom index (4942) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


But I think I included it the right way:


; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "amber03.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "amber03.ff/ions.itp"

#include "amber03.ff/dum.itp"
#ifdef POSRES
#include "posre_memb.itp"
#endif



In my coordiate file the difference between them look like this:

313LEU   HD23 4938   3.813   4.505   3.308
  313LEU  C 4939   3.435   4.335   3.190
  313LEUOC1 4940   3.429   4.330   3.090
  313LEUOC2 4941   3.337   4.305   3.259
  314DUMDUM 4942   1.996   2.371   6.171
  314DUMDUM 4943   1.996   2.371   6.271
  314DUMDUM 4944   1.996   2.471   6.171
  314DUMDUM 4945   1.996   2.471   6.271


my restraint file for the protein looks like this:


; position restraints for Protein-H of GROup of MAchos and Cynical Suckers

[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
   41   1000   1000   1000
   71   1000   1000   1000
  101   1000   1000   1000
  131   1000   1000   1000


and my restraint file for the dummy atoms look like this:

; position restraints for Protein-H of GROup of MAchos and Cynical Suckers

[ position_restraints ]
;  i funct   fcxfcyfcz
49421   1000   1000   1000
49431   1000   1000   1000
49441   1000   1000   1000
49451   1000   1000   1000


What is wrong?

Thank you for your help!!
Eva



>
>
> On 7/7/12 8:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I want do to an energy minimization and simulation with position
>> restraints.
>> Additionally to the protein I have a membrane around my protein which I
>> also ant to fix. If I won't fix it, it is in the whole box after the
>> minimization and simulation but not around my protein.
>> Since I only want the hydrogen atoms to be flexible I use the second
>> option "protein-h" when I was asked by genrestr. This makes that the
>> whole
>> protein including the membrane of dummy atoms is fix.
>> But when I want to use grompp I get the error:
>>
>> Atom index (4942) in position_restraints out of bounds (1-4941).
>> This probably means that you have inserted topology section
>> "position_restraints"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "position_restraints" section to the right
>> molecule.
>>
>>
>> The first 4941 atoms are of the "real" protein without the membrane and
>> after this the membrane starts:
>>
>>   313LEUOC1 4940   3.429   4.330   3.090
>>313LEUOC2 4941   3.337   4.305   3.259
>>314DUMDUM 4942   1.996   2.371   6.171
>>315DUMDUM 4943   1.996   2.371   6.271
>>316DUMDUM 4944   1.996   2.471   6.171
>>
>>
>> When I remove the restriction of the DUM atoms I don't get the error but
>> that is not what I want.
>>
>> Can you please tell me how I can fix the membrane?
>>
>
> You need a separate position restraint .itp file.  As the error message
> states,
> position restraints are only applicable per [moleculetype].
>
> http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] error in grompp

[Justin A. Lemkul]

On 7/7/12 8:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi everybody,
I want do to an energy minimization and simulation with position restraints.
Additionally to the protein I have a membrane around my protein which I
also ant to fix. If I won't fix it, it is in the whole box after the
minimization and simulation but not around my protein.
Since I only want the hydrogen atoms to be flexible I use the second
option "protein-h" when I was asked by genrestr. This makes that the whole
protein including the membrane of dummy atoms is fix.
But when I want to use grompp I get the error:

Atom index (4942) in position_restraints out of bounds (1-4941).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


The first 4941 atoms are of the "real" protein without the membrane and
after this the membrane starts:

  313LEUOC1 4940   3.429   4.330   3.090
   313LEUOC2 4941   3.337   4.305   3.259
   314DUMDUM 4942   1.996   2.371   6.171
   315DUMDUM 4943   1.996   2.371   6.271
   316DUMDUM 4944   1.996   2.471   6.171


When I remove the restriction of the DUM atoms I don't get the error but
that is not what I want.

Can you please tell me how I can fix the membrane?



You need a separate position restraint .itp file.  As the error message states, 
position restraints are only applicable per [moleculetype].


http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] error in grompp

[reisingere]

Hi everybody,
I want do to an energy minimization and simulation with position restraints.
Additionally to the protein I have a membrane around my protein which I
also ant to fix. If I won't fix it, it is in the whole box after the
minimization and simulation but not around my protein.
Since I only want the hydrogen atoms to be flexible I use the second
option "protein-h" when I was asked by genrestr. This makes that the whole
protein including the membrane of dummy atoms is fix.
But when I want to use grompp I get the error:

Atom index (4942) in position_restraints out of bounds (1-4941).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


The first 4941 atoms are of the "real" protein without the membrane and
after this the membrane starts:

 313LEUOC1 4940   3.429   4.330   3.090
  313LEUOC2 4941   3.337   4.305   3.259
  314DUMDUM 4942   1.996   2.371   6.171
  315DUMDUM 4943   1.996   2.371   6.271
  316DUMDUM 4944   1.996   2.471   6.171


When I remove the restriction of the DUM atoms I don't get the error but
that is not what I want.

Can you please tell me how I can fix the membrane?

Thank you,
Eva

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Re: [gmx-users] error in grompp run

[reisingere]

> On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi,
>> I want to do a MD simulation in vacuum.
>
> So don't turn on implicit solvent.
Sorry,
my fault. I want to do it in implicit solvent.
>
>>   So first I wanted to prepare the
>> files for that with "grompp".
>> But there I got the error that
>> "With GBSA implicit solvent, rgbradii must be equal to rlist"
>>
>> But the 2 values are the same in my .mdp file. Can you please show me
>> where the failure is?
>>
>>
>> define  = -DPOSRES
>> integrator  =  md
>> emtol = 1000.0
>> emstep = 0.01
>> nsteps  =  5
>> nstlist =  1
>> ns_type =  simple
>> rgbradii= 0
>> rlist   =  0
>> coulombtype =  cutoff
>> vdwtype =  cutoff
>
> These are misspelled.
>
> See manual 7.3.9 for how to simulate without cut-offs.
>
> Mark
>
>> rcoulomb=  0
>> rvdw=  0
>> pbc =  no
>> epsilon_rf  =  0
>>
>> implicit_solvent= GBSA
>> gb_algorithm= HCT
>> gb_epsilon_solvent  = 78.3
>>
>> nstxout = 1
>> nstfout = 1
>> nstvout = 1
>> nstxtcout   = 1
>> nstlog  = 1
>>
>>
>>
>> Thank you,
>> Eva
>>
>
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Re: [gmx-users] error in grompp run

[Mark Abraham]

On 13/06/2012 5:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi,
I want to do a MD simulation in vacuum.


So don't turn on implicit solvent.


  So first I wanted to prepare the
files for that with "grompp".
But there I got the error that
"With GBSA implicit solvent, rgbradii must be equal to rlist"

But the 2 values are the same in my .mdp file. Can you please show me
where the failure is?


define  = -DPOSRES
integrator  =  md
emtol = 1000.0
emstep = 0.01
nsteps  =  5
nstlist =  1
ns_type =  simple
rgbradii= 0
rlist   =  0
coulombtype =  cutoff
vdwtype =  cutoff


These are misspelled.

See manual 7.3.9 for how to simulate without cut-offs.

Mark


rcoulomb=  0
rvdw=  0
pbc =  no
epsilon_rf  =  0

implicit_solvent= GBSA
gb_algorithm= HCT
gb_epsilon_solvent  = 78.3

nstxout = 1
nstfout = 1
nstvout = 1
nstxtcout   = 1
nstlog  = 1



Thank you,
Eva



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[gmx-users] error in grompp run

[reisingere]

Hi,
I want to do a MD simulation in vacuum. So first I wanted to prepare the
files for that with "grompp".
But there I got the error that
"With GBSA implicit solvent, rgbradii must be equal to rlist"

But the 2 values are the same in my .mdp file. Can you please show me
where the failure is?


define  = -DPOSRES
integrator  =  md
emtol = 1000.0
emstep = 0.01
nsteps  =  5
nstlist =  1
ns_type =  simple
rgbradii= 0
rlist   =  0
coulombtype =  cutoff
vdwtype =  cutoff
rcoulomb=  0
rvdw=  0
pbc =  no
epsilon_rf  =  0

implicit_solvent= GBSA
gb_algorithm= HCT
gb_epsilon_solvent  = 78.3

nstxout = 1
nstfout = 1
nstvout = 1
nstxtcout   = 1
nstlog  = 1



Thank you,
Eva

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Re: [gmx-users] Error in grompp steps of position restrained

[Malai]

Dear MARK,

> Dear Mark,
>
> Thanks for mail. you mean I need to define in mdp file?.
>
>
> No. Using one of the two ways I suggested earlier depend what you're
> actually trying to do, but since your intention in using the CA group is
> unknown to us, you're preventing yourself getting specific help.
>

The error is CA index file. So my intention is to use CA group and avoid
the error. please suggest me how to use grompp or make CA index file for
grompp in position restrained step.


>
>
>  Can you please guide me how to do that. Thanks.
>
>
> http://www.gromacs.org/Documentation/File_Formats/Index_File
>

so i need to make index files for CA atoms of protein using make_ndx for
CA. can you please explain how to make index file for CA using make_ndx.

Thanks for help.


>
> Mark
>
>
> On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham wrote:
>
>>  On 8/06/2012 12:23 PM, Malai wrote:
>>
>>> Hi,
>>>
>>> After Successfully neutralizing and sd minimization of the system, I got
>>> the below error when I try the grompp for position restrained step. The
>>> command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o
>>> complx_eqn1.tpr
>>>
>>> Any help will be highly appreciated.
>>>
>>> Many thanks.
>>>
>>>
>>> Error message:
>>>
>>> ---
>>> Program grompp, VERSION 4.5.5
>>> Source code file: readir.c, line: 1320
>>>
>>> Fatal error:
>>> Group CA not found in index file.
>>> Group names must match either [moleculetype] names
>>> or custom index group names,in which case you
>>> must supply an index file to the '-n' option of grompp.
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> ---
>>>
>>
>>  Your .mdp file referred to a group for which grompp could find no
>> definition. Choose a better group or make a definition.
>>
>> Mark
>> --
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>
>
>
>
>
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Re: [gmx-users] Error in grompp steps of position restrained

[Mark Abraham]

On 8/06/2012 12:34 PM, Malai wrote:

Dear Mark,

Thanks for mail. you mean I need to define in mdp file?.


No. Using one of the two ways I suggested earlier depend what you're 
actually trying to do, but since your intention in using the CA group is 
unknown to us, you're preventing yourself getting specific help.



Can you please guide me how to do that. Thanks.


http://www.gromacs.org/Documentation/File_Formats/Index_File

Mark


On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham > wrote:


On 8/06/2012 12:23 PM, Malai wrote:

Hi,

After Successfully neutralizing and sd minimization of the
system, I got the below error when I try the grompp for
position restrained step. The command I used is :grompp -v -f
eqn1.mdp -c complx_sd.pdb -p complx.top -o complx_eqn1.tpr

Any help will be highly appreciated.

Many thanks.


Error message:

---
Program grompp, VERSION 4.5.5
Source code file: readir.c, line: 1320

Fatal error:
Group CA not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp.
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


Your .mdp file referred to a group for which grompp could find no
definition. Choose a better group or make a definition.

Mark
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Re: [gmx-users] Error in grompp steps of position restrained

[Malai]

Dear Mark,

Thanks for mail. you mean I need to define in mdp file?. Can you please
guide me how to do that. Thanks.

On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham wrote:

> On 8/06/2012 12:23 PM, Malai wrote:
>
>> Hi,
>>
>> After Successfully neutralizing and sd minimization of the system, I got
>> the below error when I try the grompp for position restrained step. The
>> command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o
>> complx_eqn1.tpr
>>
>> Any help will be highly appreciated.
>>
>> Many thanks.
>>
>>
>> Error message:
>>
>> --**-
>> Program grompp, VERSION 4.5.5
>> Source code file: readir.c, line: 1320
>>
>> Fatal error:
>> Group CA not found in index file.
>> Group names must match either [moleculetype] names
>> or custom index group names,in which case you
>> must supply an index file to the '-n' option of grompp.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>> --**-
>>
>
> Your .mdp file referred to a group for which grompp could find no
> definition. Choose a better group or make a definition.
>
> Mark
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Re: [gmx-users] Error in grompp steps of position restrained

[Mark Abraham]

On 8/06/2012 12:23 PM, Malai wrote:

Hi,

After Successfully neutralizing and sd minimization of the system, I 
got the below error when I try the grompp for position restrained 
step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p 
complx.top -o complx_eqn1.tpr


Any help will be highly appreciated.

Many thanks.


Error message:

---
Program grompp, VERSION 4.5.5
Source code file: readir.c, line: 1320

Fatal error:
Group CA not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp.
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---


Your .mdp file referred to a group for which grompp could find no 
definition. Choose a better group or make a definition.


Mark
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[gmx-users] Error in grompp steps of position restrained

[Malai]

Hi,

After Successfully neutralizing and sd minimization of the system, I got
the below error when I try the grompp for position restrained step. The
command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o
complx_eqn1.tpr

Any help will be highly appreciated.

Many thanks.


Error message:

---
Program grompp, VERSION 4.5.5
Source code file: readir.c, line: 1320

Fatal error:
Group CA not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
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Re: [gmx-users] error in grompp

[Justin A. Lemkul]

Serena Leone wrote:

Hi all

I am trying to model a sulfated octasaccharide. I retrieved the topology 
files from prodrg and I fixed them. The same procedure on a the 
monosaccharide unit of the oligosaccharide I'm going to run worked 
smoothly. After solvating the molecule, I try to pre-process it and I 
obtain the following error:


-- Generated 279 of the 1225 non-bonded parameter combinations
WARNING 1 [file "GI.top", line 993]:
 Too few parameters on line (source file toppush.c, line 1168)
processing coordinates...

---
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (GI_wb.gro, 17431)
does not match topology (GI.top, 0)


According to the wiki, the fact that no atom is recognized in the top 
points to an incorrect location of the path for the cpp in the mdp, but 
this is not the case (i double checked, plus this is exactly the same 
mdp file that i used for other runs and that worked fine...). I also 
checked for mispellings of atoms and residues names in the top, but 
everything apparently fits. Do you have any idea of what else may cause 
this behavior?


One can only blame cpp if the error messages show up as they appear on the wiki, 
but the output you've shown does not indicate that as a problem.  If this is not 
the case, there are several other possibilities.  Usually it's something simple, 
like a type in an #include line, or including the relevant .itp files in the 
wrong order, or something else less obvious.


It looks like there is another problem: "Too few parameters on line..." so I 
would explore that error to see if that is causing some failure in the grompp 
process.


-Justin



Thanks a lot
Cheers,
Serena



--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] error in grompp

[Serena Leone]

Hi all

I am trying to model a sulfated octasaccharide. I retrieved the 
topology files from prodrg and I fixed them. The same procedure on a 
the monosaccharide unit of the oligosaccharide I'm going to run worked 
smoothly. After solvating the molecule, I try to pre-process it and I 
obtain the following error:


-- Generated 279 of the 1225 non-bonded parameter combinations
WARNING 1 [file "GI.top", line 993]:
 Too few parameters on line (source file toppush.c, line 1168)
processing coordinates...

---
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 469

Fatal error:
number of coordinates in coordinate file (GI_wb.gro, 17431)
does not match topology (GI.top, 0)


According to the wiki, the fact that no atom is recognized in the top 
points to an incorrect location of the path for the cpp in the mdp, but 
this is not the case (i double checked, plus this is exactly the same 
mdp file that i used for other runs and that worked fine...). I also 
checked for mispellings of atoms and residues names in the top, but 
everything apparently fits. Do you have any idea of what else may cause 
this behavior?


Thanks a lot
Cheers,
Serena

--
Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel)  617-732-8586






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