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

[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)
  442ALA    HB1 6611   2.350   3.446   6.215
  442ALA    HB2 6612   2.294   3.373   6.080
  442ALA    HB3 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
  443GLY    HA1 6623   5.250   5.886   5.701
  443GLY    HA2 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";<272699575 at qq.com>;
Date:  Mon, Aug 7, 2017 07:34 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>; 
Cc:  "ZHANG Cheng"<272699575 at 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