[gmx-users] regarding pdb2gmx
Justin Lemkul
jalemkul at vt.edu
Sat May 30 14:28:21 CEST 2015
On 5/30/15 6:40 AM, soumadwip ghosh wrote:
> Hi all,
> I have a general query about the basic functioning of pdb2gmx. I
> recently observed that when I take a PDB file for a DNA molecule and build
> its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it
> without any hitches. If I look at the .itp file made for the DNA chain it
> looks like,
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB massB
> ; residue 1 DC rtp DC q -0.5
> 1 ON5 1 DC O5' 1 -0.66 15.9994 ;
> qtot -0.66
> 2 HN5 1 DC H5T 2 0.43 1.008 ;
> qtot -0.23
> 3 CN8B 1 DC C5' 3 0.05 12.011 ;
> qtot -0.18
> 4 HN8 1 DC H5'1 4 0.09 1.008 ;
> qtot -0.09
> 5 HN8 1 DC H5'2 5 0.09 1.008 ;
> qtot 0
> 6 CN7 1 DC C4' 6 0.16 12.011 ;
> qtot 0.16
> 7 HN7 1 DC H4' 7 0.09 1.008 ;
> qtot 0.25
> 8 ON6 1 DC O4' 8 -0.5 15.9994 ;
> qtot -0.25
> 9 CN7B 1 DC C1' 9 0.16 12.011 ;
> qtot -0.09
> 10 HN7 1 DC H1' 10 0.09 1.008 ;
> qtot 0
> 11 NN2 1 DC N1 11 -0.13 14.007 ;
> qtot -0.13
> 12 CN3 1 DC C6 12 0.05 12.011 ;
> qtot -0.08
> 13 HN3 1 DC H6 13 0.17 1.008 ;
> qtot 0.09
> 14 CN3 1 DC C5 14 -0.13 12.011 ;
> qtot -0.04
> 15 HN3 1 DC H5 15 0.07 1.008 ;
> qtot 0.03
> 16 CN1 1 DC C2 16 0.52 12.011 ;
> qtot 0.55
> 17 ON1C 1 DC O2 17 -0.49 15.9994 ;
> qtot 0.06
> 18 NN3 1 DC N3 18 -0.66 14.007 ;
> qtot -0.6
> 19 CN2 1 DC C4 19 0.65 12.011 ;
> qtot 0.05
> 20 NN1 1 DC N4 20 -0.75 14.007 ;
> qtot -0.7
> 21 HN1 1 DC H41 21 0.37 1.008 ;
> qtot -0.33
> 22 HN1 1 DC H42 22 0.33 1.008 ;
> qtot 0
> 23 CN8 1 DC C2' 23 -0.18 12.011 ;
> qtot -0.18
> 24 HN8 1 DC H2'1 24 0.09 1.008 ;
> qtot -0.09
> 25 HN8 1 DC H2'2 25 0.09 1.008 ;
> qtot 0
> 26 CN7 1 DC C3' 26 0.01 12.011 ;
> qtot 0.01
> 27 HN7 1 DC H3' 27 0.09 1.008 ;
> qtot 0.1
> 28 ON2 1 DC O3' 28 -0.57 15.9994 ;
> qtot -0.47
> For one residue.
> However, if you look at the [ bond ] section of this .itp file it looks
> like,
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 3 4 1
> 3 5 1
> 3 6 1
> 6 7 1
> 6 8 1
> 6 26 1
> 8 9 1
> 9 10 1
> 9 11 1
> 9 23 1
> 11 12 1
> 11 16 1
> 12 13 1
> There are no parameters in the right and by principle grompp should
> complain about this. But the simulation runs fine and the proper
> interactions with the desired outcomes are always obtained. However, things
> get altered when I proceed to model anything else than a DNA/protein. As
> for example, I have made a topology for tetramethyl ammonium ion ( in
> CHARMM 27) and as usual it lacks these parameters in all the [ bonds ],
> {angle ] or [ dihedral ] sections. I changed the .top extension to tma.itp
> and included in the system topology for a double stranded DNA molecule
> according to standard protocols. Now when I start grompp it screams about
> the 'missing parameters in the tma.itp ffile'. My question is everytime I
> model something my CHARMM, do I have to include parameters such as force
> constant, phi0, b0, mult etc from the ffbonded.itp file manually or does
> pdb2gmx should write it looking at the connectivity mentioned in the PDB
> file? The same thing goes for writing sigma and epsilon terms from the
> ffnonbonde.itp file manually or pdb2gmx should do it by default? I have
> another question that is it ok not to specify the [ atomtypes ] and [
> pairtypes ] in the .itp file because without these being specified
> properly, is it possible that the correct non bonding interaction arises? I
> have always seen SWISSPARAM and ATB topologies come with all these things
> mentioned from the scratch but with pdb2gmx I have never seen it. So, is it
> like pdb2gmx gives only the atoms making the bonds, angles, prop and
> improp. dihedrals (atomtypes already mentioned in the aminoacids.rtp file)
> and the rest of the parameters are to placed manually or am i missing
> something regarding pdb2gmx( some flags)??
> Recently, I wanted to simulate graphene and although the ideal job is to go
> with g_x2top, issuing pdb2gmx should also work right? The topology is
> getting formed but without the c0, c1, c2...etc parameters. I dig up the
> ffbonded and ffnonboned.itp files from the CHARMM27.ff library and have
> manually placed them. It no longer shows an error but I'm still not assured
> whether the correct interaction would arise or not.
>
> If anyone can spare some of their times and help me understand this I would
> be highly obliged. Sorry if I am asking for much.
>
The grompp hierarchy is such that it (1) uses any parameters it finds explicitly
listed in the .top, (2) searches for any that aren't listed in ffbonded.itp, and
(3) throws a fatal error if it can't find any. So it is entirely normal for
there to be no parameters listed in the .top (this is actually how all the force
fields work except GROMOS). If you're playing around with non-standard
molecules, some parameters may not exist in the parent force field (note that
the CHARMM27 force field in GROMACS does not support CGenFF like our CHARMM36
port does, so its chemical space is more limited).
-Justin
--
==================================================
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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