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";<272699...@qq.com>; Date: Mon, Aug 7, 2017 07:34 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
