[gmx-users] Minimization Problem

2017-10-09 Thread Ednilsom Orestes 
Dear Gromacs community

I am trying to run a simulation of choline molecule but found various
errors concerning to bonds, angles and dihedrals during the minimization.



Part of the top file (line number in the first column):
...
29 [ bonds ]
30;  aiaj funct
311  4 1; N   CT3
32114 1; N   CT4
331  2 1; N   CT1
341  3 1; N   CT2
35212 1;   CT1  HC12
36213 1;   CT1  HC11
37211 1;   CT1  HC13
383  7 1;   CT2  HC21
393  6 1;   CT2  HC22
403  5 1;   CT2  HC23
414  8 1;   CT3  HC31
42410 1;   CT3  HC32
434  9 1;   CT3  HC33
44   1417 1;   CT4  HC41
45   1415 1;   CT4   CT5
46   1416 1;   CT4  HC42
47   1520 1;   CT5  HC51
48   1518 1;   CT5OH
49   1519 1;   CT5  HC52
50   2118 1;HOOH
...


Errors:

ERROR 1 [file topol_choline.top, line 49]:
No Default Bond type

ERROR 2 [file topol_choline.top, line50]:
No Default Bond type

and so on with some of the angles and dihedrals...

Does anybody have a clue on how to fix it?

Thanks in advance.

Ednilsom
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Re: [gmx-users] Ionic liquid simulation problem

2017-09-06 Thread Ednilsom Orestes 
Hi Ghosh,

Thanks for your answer.
But I'm not sure if I understood what you meant.
I already used insert-molecules command to create a box with the cationic
species.
Now, should I use the same command to include the anionic species into the
box?

Best



*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*

*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
Cecília*
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777*


2017-09-05 17:24 GMT-03:00 soumadwip ghosh :

> Hi,
>
> I am not sure why you used the gmx solvate command for putting the
> anionic species in your simulation box. It is meant for filling up the
> simulation box with water molceules as the resname 'SOL' in the
> topol.top file. Thus when you hit grompp it expects 'SOL' entry in
> your topology file, cant find it and prints an error. In my opinion,
> one should use the same gmx insert-molecules command for inserting the
> anionic part into the box. If you dont want to use water in the
> simulation you can proceed without the solvation step but cant use gmx
> solvate for inserting anionic species or anything else.
>
> Best
> Soumadwip Ghosh
> Post Doctoral Research Associate
> City of Hope Cancer Research Center
> Duarte 91010 CA
> USA
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[gmx-users] Fwd: Ionic liquid simulation problem.

2017-09-05 Thread Ednilsom Orestes 
*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*

*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
Cecília*
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777*


-- Forwarded message --
From: Ednilsom Orestes <eores...@gmail.com>
Date: 2017-09-05 15:32 GMT-03:00
Subject: Ionic liquid simulation problem.
To: gromacs.org_gmx-users@maillist.sys.kth.se


Dear GROMACS Community,

I am very new with GROMACS I am trying to run a simulation of an ionic
liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to
the following protocol:

1. Prepared the respective PDB files and added/modified the OPLS/AA force
field parameters updating the atomtypes.atp, aminoacid.rtp, ffbonded.itp
and ffnonbonded.itp files.

2. Used *pdb2gmx* command to create the respective .gro files, as well as,
the posre.itp and topol.top files chossing OPLS/AA option without solvation.

3. Used the *insert-molecules* command to create a box filled with one
specie (cation) and used the *solva**te* command to add the other specie
(anion) as solvent into the same box.

4. Updated, by hand, the generated topol_box.top (pos_box.top) file
including the topol.top and the posre.itp files of the other specie (anion)
at the end of it.

5. I them tried to used the *grompp* command to minimize the energy of the
cations+anions box and got the following error:

Fatal error:
Syntax error – File forcefield.itp, line 20
Last line read:
‘1 3yes   0.5  0.5'
Found a second defaut directive.

Does anyone knows whats is wrong with such a protocol?

Thanks in advance.

Ednilsom



*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*

*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
Cecília*
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777 <+55%2024%202107-3777>*
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[gmx-users] Ionic liquid simulation problem.

2017-09-05 Thread Ednilsom Orestes 
Dear GROMACS Community,

I am very new with GROMACS I am trying to run a simulation of an ionic
liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to
the following protocol:

1. Prepared the respective PDB files and added/modified the OPLS/AA force
field parameters updating the atomtypes.atp, aminoacid.rtp, ffbonded.itp
and ffnonbonded.itp files.

2. Used *pdb2gmx* command to create the respective .gro files, as well as,
the posre.itp and topol.top files chossing OPLS/AA option without solvation.

3. Used the *insert-molecules* command to create a box filled with one
specie (cation) and used the *solva**te* command to add the other specie
(anion) as solvent into the same box.

4. Updated, by hand, the generated topol_box.top (pos_box.top) file
including the topol.top and the posre.itp files of the other specie (anion)
at the end of it.

5. I them tried to used the *grompp* command to minimize the energy of the
cations+anions box and got the following error:

Fatal error:
Syntax error – File forcefield.itp, line 20
Last line read:
‘1 3yes   0.5  0.5'
Found a second defaut directive.

Does anyone knows whats is wrong with such a protocol?

Thanks in advance.

Ednilsom



*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*

*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
Cecília*
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777*
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