Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

2017-08-07 Thread ZHANG Cheng 
Dear Yujie Liu,
Can I clarify your suggestions?


copy gly.gro into protein.gro and changed the number of atoms:
) After running "gmx insert-molecules -ci gly.gro -nmol 10 -f 
protein_newbox.gro -o protein_glycine.gro",
the "protein_glycine.gro" already contains both protein residues and glycine 
ones, with 10 glycines following the proteins residues, as if they belong to a 
same molecule as shown below, so I can assume it is already copied as you 
suggested?


  (.. protein residues from 1 to 442)
  442ALAHB1 6611   2.350   3.446   6.215
  442ALAHB2 6612   2.294   3.373   6.080
  442ALAHB3 6613   2.225   3.341   6.225
  442ALA  C 6614   2.443   3.233   6.346
  442ALA OT 6615   2.357   3.205   6.425
  442ALA  O 6616   2.556   3.249   6.383
  442ALA HO 6617   2.561   3.236   6.483
  443GLY  N 6618   5.163   5.878   5.519
  443GLY H1 6619   5.235   5.930   5.475
  443GLY H2 6620   5.179   5.780   5.507
  443GLY H3 6621   5.075   5.902   5.479
  443GLY CA 6622   5.160   5.910   5.663
  443GLYHA1 6623   5.250   5.886   5.701
  443GLYHA2 6624   5.145   6.008   5.672
  443GLY  C 6625   5.052   5.834   5.736
  443GLY OT 6626   5.046   5.831   5.857
  443GLY  O 6627   4.965   5.774   5.662
  443GLY HO 6628   4.898   5.727   5.720
  (.. glycine molecules from 443 to 452)
  10.88213  10.88213  10.88213 (this is the dimension of the box)


-


Then using #include??  ?? lines to add gly.itp into protein.top in suitable 
position 
) Do you mean in the protein.top file, change


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


into


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


?


-
changed [molecules] options to add the name and number of gly molecule. Note 
the information of posre_gly.itp.
) Do you mean in the protein.top file, change


[ molecules ]
; Compound#mols
Protein_chain_L 1


into


[ molecules ]
; Compound#mols
Protein_chain_L 1   (the "Protein_chain_L" refers to the protein)
Protein 10  (the "Protein" refers to the glycine)


?





-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Mon, Aug 7, 2017 07:34 PM
To:  "gromacs.org_gmx-users"; 
Cc:  "ZHANG Cheng"<272699...@qq.com>; 
Subject:  How to configure the gro/itp/top files after running 
"insert-molecules"?



Dear Gromacs,
I am doing a MD for a protein with glycines.


For glycine, I use 
) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter
and got 
) gly.gro
) posre_gly.itp
) topol_gly.top


For protein, I use
) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh 
-merge interactive
) gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt 
cubic
and got
) protein_processed.gro
) posre_protein.itp
) topol_protein.top

) protein_newbox.gro


Then, I add glycines to the protein box:
) gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o 
protein_glycine.gro
and got
) protein_glycine.gro, in which the 10 glycines were appended to the protein 
residues, as if they belong to the same protein molecule (is this normal?)


Can I ask,
1) How can I configure the itp and top files (i.e. posre_gly.itp, 
topol_gly.top, posre_protein.itp, topol_protein.top), so as to proceed my MD 
setting-up? E.g. should I combine them into one itp and one top file, how to do 
that?
2) Then, I will fill the box with water, then add Na+/Cl- ions, then energy 
minimization. Is this the correct procedure?


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

2017-08-07 Thread Souvik Dey 
But what if the coordinates do not match? I mean Glycine may not have the
same coordinates after.

On Mon, Aug 7, 2017 at 2:48 PM, yujie liu  wrote:

>
> The .top file of protein has included itself all parameters, so now you
> only copy gly.gro into protein.gro and changed the number of atoms. Then
> using #include”  ” lines to add gly.itp into protein.top in suitable
> position and changed [molecules] options to add the name and number of gly
> molecule. Note the information of posre_gly.itp.
> --
> Gromacs Users mailing list
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-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

2017-08-07 Thread ZHANG Cheng 
Dear Gromacs,
I am doing a MD for a protein with glycines.


For glycine, I use 
) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter
and got 
) gly.gro
) posre_gly.itp
) topol_gly.top


For protein, I use
) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh 
-merge interactive
) gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt 
cubic
and got
) protein_processed.gro
) posre_protein.itp
) topol_protein.top

) protein_newbox.gro


Then, I add glycines to the protein box:
) gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o 
protein_glycine.gro
and got
) protein_glycine.gro, in which the 10 glycines were appended to the protein 
residues, as if they belong to the same protein molecule (is this normal?)


Can I ask,
1) How can I configure the itp and top files (i.e. posre_gly.itp, 
topol_gly.top, posre_protein.itp, topol_protein.top), so as to proceed my MD 
setting-up? E.g. should I combine them into one itp and one top file, how to do 
that?
2) Then, I will fill the box with water, then add Na+/Cl- ions, then energy 
minimization. Is this the correct procedure?


Thank you.


Yours sincerely
Cheng
-- 
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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