Dear users, I am studying the dynamics of a double stranded DNA in presence of choline counterion. I am using GROMACS 4.5.6 and CHARMM27 force field for MD simulations. Initially, I made the united atom PDB for Choline using ATB topology biliding software. Since the PDB was specifically meant for GROMOS forcefield, I copied the PDB in my working directory and added [ CHO ] in the aminoacid.rtp according to the ones specified in atomtypes.atp of CHARMM27 force field directory. My PDB file looks like -
DER UNCLASSIFIED 05-Dec-14 TITLE UNITED ATOM STRUCTURE FOR MOLECULE CHO AUTHOR GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2014-09-22 AUTHOR 2 http://compbio.biosci.uq.edu.au/atb HETATM 1 O6 CHO 0 -2.169 0.657 0.155 1.00 0.00 O HETATM 2 H14 CHO 0 -3.029 0.566 0.595 1.00 0.00 H HETATM 3 C4 CHO 0 -1.635 -0.644 -0.037 1.00 0.00 C HETATM 4 C5 CHO 0 -0.300 -0.549 -0.758 1.00 0.00 C HETATM 5 N1 CHO 0 0.876 0.042 0.022 1.00 0.00 N1+ HETATM 6 C8 CHO 0 2.088 -0.022 -0.875 1.00 0.00 C HETATM 7 C7 CHO 0 0.630 1.486 0.391 1.00 0.00 C HETATM 8 C6 CH0 0 1.156 -0.753 1.269 1.00 0.00 C CONECT 1 2 3 CONECT 2 1 CONECT 3 1 4 CONECT 4 3 5 CONECT 5 4 6 7 8 CONECT 6 5 CONECT 7 5 CONECT 8 5 END The [ choline ] part in aminoacid.rtp looks like- [ CHO ] [ atoms ] O6 OH1 -0.66 1 H14 H 0.31 2 C4 CTL2 0.30 3 C5 CTL2 0.30 4 N1 NH3 -0.30 5 C8 CTL5 0.35 6 C7 CTL5 0.35 7 C6 CTL5 0.35 8 [ bonds ] O6 H14 O6 C4 H14 O6 C4 O6 C4 C5 C5 N1 C8 N1 C7 N1 C6 N1 Then I did pdb2gmx -f cholineua.pdb to make the topology of choline. It proceeded smoothly and I made the choline.itp file from the .top file created and it looks like- File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Fri Dec 5 04:28:53 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.6 ; ; Command line was: ; pdb2gmx -f cholineua.pdb ; ; Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters [ moleculetype ] ; Name nrexcl CHO 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 0 CHO rtp CHO q +1.0 1 OH1 0 CHO O6 1 -0.66 15.999 ; qtot -0.66 2 H 0 CHO H14 2 0.31 1.008 ; qtot -0.35 3 CTL2 0 CHO C4 3 0.3 12.011 ; qtot -0.05 4 CTL2 0 CHO C5 4 0.3 12.011 ; qtot 0.25 5 NH3 0 CHO N1 5 -0.3 14.007 ; qtot -0.05 6 CTL5 0 CHO C8 6 0.35 12.011 ; qtot 0.3 7 CTL5 0 CHO C7 7 0.35 12.011 ; qtot 0.65 8 CTL5 0 CHO C6 8 0.35 12.011 ; qtot 1 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 3 4 1 4 5 1 5 6 1 5 7 1 5 8 1 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 5 1 2 4 1 3 6 1 3 7 1 3 8 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 5 1 3 4 5 3 4 5 5 4 5 6 5 4 5 7 5 4 5 8 5 6 5 7 5 6 5 8 5 7 5 8 5 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 3 4 9 1 3 4 5 9 3 4 5 6 9 3 4 5 7 9 3 4 5 8 9 ; Include Position restraint file #ifdef POSRES #include "posrecholine.itp" #endif Now when I include this itp file to the DNA.pdb upto ci and nmol part there is no problem and I can insert the desired no. of choline molecules in the system. But when I am calling grompp for the first time, it shows errors like too few parameters in the cholineua.itp files, no defined dihedral, no bond UB type, and so on...... Is this because the c0 c1 c2 parameters are not there in my .itp file? If this is the case, then this .itp file can't be used. So I looked for Paramchem and Swissparam topology builder which is compatible with CHARMM. They are known to provide accurate topology parameters. But I dont know how to use them. The Paramchem requires a .mol2 version of input. But I have this PDB which is not generating any .str file from Paramchem. There are certain problem with my university internet connections and all the time I am not getting connected with these sites. Can anybody provide me a .itp file for choline molecule which can be used in CHARMM? It may/may not be based on the pdb file which I am using. I am having difficulties in network connections and I need this correct choline.itp urgently so that I can proceed with my project. Alternatively how to tackle the error which I mentioned while executing GROMPP ? Any kind of help will be hugely appreciated. Thanks for your time in advance. Regards, Soumadwip Ghosh Research fellow Indian Institute of Technology, Bombay India -- 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.