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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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