[gmx-users] .itp file of choline molecule
Justin Lemkul
jalemkul at vt.edu
Sun Dec 7 14:18:08 CET 2014
On 12/7/14 3:48 AM, soumadwip ghosh wrote:
> 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......
>
Don't use this hacked topology. It is incorrect to try to make a united-atom
topology in this way. Choline is well defined as an all-atom entity in the
CHARMM force fields and it is already a part of the force field port we create
for Gromacs:
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
This version of choline is the model compound used by CGenFF, so you should
change the atom types back to the CHARMM36 lipid force field by obtaining the
CHARMM force field files:
http://mackerell.umaryland.edu/charmm_ff.shtml#charmm
(see stream/toppar_all36_lipid_model.str) and modifying the atom types accordingly.
-Justin
>
> 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
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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