[gmx-users] Need to confirm parameters.
Justin Lemkul
jalemkul at vt.edu
Wed May 31 13:55:02 CEST 2017
On 5/31/17 2:26 AM, Sailesh Bataju wrote:
>> Extract the coordinates of any valine side chain in a protein, make an IBUT .hdb
>> entry based off of it (all you'll need to do is change 2 -> 3 in the number of H
>> added to the CB atom) and submit to pdb2gmx; it will build any missing H atoms
>> for you.
>
>> -Justin
>
> I did exactly you said and topology files were generated. The output
> of the terminal is:
>
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
> Reading test2_edited.pdb...
> Read 'ALKANE ISOMER OF N-BUTANE', 13 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 1 residues with 13 atoms
>
> chain #res #atoms
> 1 'A' 1 13
>
> All occupancies are one
> Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
> Atomtype 412
> Reading residue database... (charmm36)
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.rtp
> Residue 1025
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.hdb
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.n.tdb
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.5#
> Processing chain 1 'A' (13 atoms, 1 residues)
> Warning: Starting residue IBU1 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
> Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.arn
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 1 residues with 14 atoms
> Making bonds...
> Number of bonds was 13, now 13
> Generating angles, dihedrals and pairs...
> Before cleaning: 27 pairs
> Before cleaning: 27 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...
> There are 27 dihedrals, 0 impropers, 24 angles
> 27 pairs, 13 bonds and 0 virtual sites
> Total mass 58.124 a.m.u.
> Total charge 0.000 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.1#
>
> Writing coordinate file...
> --------- PLEASE NOTE ------------
> You have successfully generated a topology from: test2_edited.pdb.
> The Charmm36 force field and the tip3p water model are used.
> --------- ETON ESAELP ------------
>
> But the topol.top file looks empty. The topol.top file is:
>
> ; Include forcefield parameters
> #include "charmm36.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Alkane_chain_A 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> ; residue 1 IBU rtp IBU q 0.0
> 1 CC31A 1 IBU CT 1 -0.09 12.011
> ; qtot -0.09
> 2 HCA1A 1 IBU HT 2 0.09 1.008 ; qtot 0
> 3 CC33A 1 IBU C1 3 -0.27 12.011
> ; qtot -0.27
> 4 HCA3A 1 IBU H11 4 0.09 1.008
> ; qtot -0.18
> 5 HCA3A 1 IBU H12 5 0.09 1.008
> ; qtot -0.09
> 6 HCA3A 1 IBU H13 6 0.09 1.008 ; qtot 0
> 7 CC33A 1 IBU C2 7 -0.27 12.011
> ; qtot -0.27
> 8 HCA3A 1 IBU H21 8 0.09 1.008
> ; qtot -0.18
> 9 HCA3A 1 IBU H22 9 0.09 1.008
> ; qtot -0.09
> 10 HCA3A 1 IBU H23 10 0.09 1.008 ; qtot 0
> 11 CC33A 1 IBU C3 11 -0.27 12.011
> ; qtot -0.27
> 12 HCA3A 1 IBU H31 12 0.09 1.008
> ; qtot -0.18
> 13 HCA3A 1 IBU H32 13 0.09 1.008
> ; qtot -0.09
> 14 HCA3A 1 IBU H33 14 0.09 1.008 ; qtot 0
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 7 1
> 1 11 1
> 3 4 1
> 3 5 1
> 3 6 1
> 7 8 1
> 7 9 1
> 7 10 1
> 11 12 1
> 11 13 1
> 11 14 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 2 4 1
> 2 5 1
> 2 6 1
> 2 8 1
> 2 9 1
> 2 10 1
> 2 12 1
> 2 13 1
> 2 14 1
> 3 8 1
> 3 9 1
> 3 10 1
> 3 12 1
> 3 13 1
> 3 14 1
> 4 7 1
> 4 11 1
> 5 7 1
> 5 11 1
> 6 7 1
> 6 11 1
> 7 12 1
> 7 13 1
> 7 14 1
> 8 11 1
> 9 11 1
> 10 11 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 3 5
> 2 1 7 5
> 2 1 11 5
> 3 1 7 5
> 3 1 11 5
> 7 1 11 5
> 1 3 4 5
> 1 3 5 5
> 1 3 6 5
> 4 3 5 5
> 4 3 6 5
> 5 3 6 5
> 1 7 8 5
> 1 7 9 5
> 1 7 10 5
> 8 7 9 5
> 8 7 10 5
> 9 7 10 5
> 1 11 12 5
> 1 11 13 5
> 1 11 14 5
> 12 11 13 5
> 12 11 14 5
> 13 11 14 5
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 2 1 3 4 9
> 2 1 3 5 9
> 2 1 3 6 9
> 7 1 3 4 9
> 7 1 3 5 9
> 7 1 3 6 9
> 11 1 3 4 9
> 11 1 3 5 9
> 11 1 3 6 9
> 2 1 7 8 9
> 2 1 7 9 9
> 2 1 7 10 9
> 3 1 7 8 9
> 3 1 7 9 9
> 3 1 7 10 9
> 11 1 7 8 9
> 11 1 7 9 9
> 11 1 7 10 9
> 2 1 11 12 9
> 2 1 11 13 9
> 2 1 11 14 9
> 3 1 11 12 9
> 3 1 11 13 9
> 3 1 11 14 9
> 7 1 11 12 9
> 7 1 11 13 9
> 7 1 11 14 9
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "charmm36.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "charmm36.ff/ions.itp"
>
> [ system ]
> ; Name
> ALKANE ISOMER OF N-BUTANE
>
> [ molecules ]
> ; Compound #mols
> Alkane_chain_A 1
>
> I think [bonds], [pairs],etc section should be automatically filled
> up. Did I do something wrong?
>
No, that's perfectly normal. Parameter values are referenced from the force
field and are not explicitly printed to the .top file.
-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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