[gmx-users] Difficulty preparing a polymer (PEG) for simulation.
Justin Lemkul
jalemkul at vt.edu
Thu Mar 27 15:04:51 CET 2014
On 3/27/14, 9:54 AM, Dan Sponseller wrote:
> I’m trying to prepare PEG for simulation in gromacs and running into considerable difficulties. My PEG chain is
>
> HOC-COC-COC…...COC-COC-COH
>
> with appropriate hydrogens on the carbons. I am using the new CHARM36.ff Following the procedure for polymers, I added a beginning, and end, and a central chain piece to ‘merged.rtp’ and modified the atom names in the .pdb file to match. I have also added the residues to the ‘residuetypes.dat’ as Non-Protein (I have also tried listing it as a Protein).
>
"Non-Protein" is not going to be recognized in residuetypes.dat. Use "Other" or
"Protein."
> pdb2gmx claims I have169 missing atoms but will create the .gro and .top files anyway with the -missing parameter passed. The .gro file has all the atoms but the .top seems to be missing much information on bonds and angles. Probably no point in continuing but after a quick editconfig, grompp gives me a fatal error: Group Protein referenced in the .mdp file was not found in the index file.
>
Your input .pdb file has numerous problems. See below. I can think of only one
appropriate use for -missing, and it's not here :)
The fact that "Protein" is not found indicates you're using an .mdp file
designed for simulating a protein, but your attempt to use "Non-Protein" above
clearly contradicts any definition of the polymer as "Protein."
> I am new to gromacs and would really appreciate help getting started on its use like this. Following is some of my data files.
>
> Daniel Sponseller
> PhD student
> Computational Science and Informatics
> George Mason University
>
>
>
> ********************************************************************************
> Snip from ‘merged.rtp’
>
> ;Dan Sponseller
> ;Copying from DME below for the repeating chain for PEG.
> [ LIG ]
> [ atoms ]
> C1 CC32A -0.010 0
> H11 HCA2A 0.090 1
> H12 HCA2A 0.090 2
> OO2 OC30A -0.340 3
> C3 CC32A -0.010 4
> H31 HCA2A 0.090 5
> H32 HCA2A 0.090 6
> [ bonds ]
> C1 -C3
> C1 H11
> C1 H12
> C1 OO2
> OO2 C3
> C3 H31
> C3 H32
> C3 +C1
>
> ;Dan Sponseller
> ;Next, define begining of chain for PEG. CH2-OH from [ ETOH ]
> [ LIGb ]
> [ atoms ]
> OO1 OG311 -0.650 0
> H11 HGP1 0.420 1
> C3 CG321 0.050 2
> H31 HGA2 0.090 3
> H32 HGA2 0.090 4
> [ bonds ]
> OO1 H11
> OO1 C3
> C3 H31
> C3 H32
> C3 +C1
>
> ;Dan Sponseller
> ;Next, define ending of chain for PEG. CH2-OH from [ ETOH ]
> [ LIGe ]
> [ atoms ]
> C1 CG321 0.050 0
> H11 HGA2 0.090 1
> H12 HGA2 0.090 2
> OO2 OG311 -0.650 3
> H21 HGP1 0.420 4
> [ bonds ]
> C1 -C3
> C1 H11
> C1 H12
> C1 OO2
> OO2 H21
>
> ********************************************************************************
> my modified ‘PEG.pdb’ file:
>
> COMPND UNNAMED
> AUTHOR GENERATED BY OPEN BABEL
> HETATM 1 C1 LIGe 1 -14.784 -1.665 0.506 1.00 0.00 C
> HETATM 2 C3 LIG 2 -13.927 -1.410 -0.735 1.00 0.00 C
> HETATM 3 OO2 LIG 2 -13.056 -0.302 -0.493 1.00 0.00 O
> HETATM 4 H11 LIGe 1 -15.383 -2.563 0.355 1.00 0.00 H
> HETATM 5 H12 LIGe 1 -14.137 -1.802 1.372 1.00 0.00 H
Problem #1 - you're beginning the chain with the ending residue. In the
scenario above, the chain should start (residue 1) with LIGb and end with LIGe.
Problem #2 - you've got discontinuous residues. You can't start LIGe, then mix
in LIG, then go back to LIGe. pdb2gmx will look at the residue numbering, and
whenever it changes, it starts a new residue (i.e. its own internal numbering).
Hence you're getting missing atoms in residue 1 (LIGe), because the only atom
pdb2gmx finds is C1 before it encounters a new residue (LIG).
-Justin
> HETATM 6 H31 LIG 2 -13.333 -2.297 -0.956 1.00 0.00 H
> HETATM 7 H32 LIG 2 -14.573 -1.185 -1.584 1.00 0.00 H
> HETATM 8 C1 LIG 2 -12.207 0.022 -1.596 1.00 0.00 C
> HETATM 9 C3 LIG 3 -11.325 1.216 -1.227 1.00 0.00 C
> HETATM 10 OO2 LIG 3 -10.441 0.845 -0.167 1.00 0.00 O
> HETATM 11 H12 LIG 2 -11.578 -0.836 -1.835 1.00 0.00 H
> HETATM 12 H11 LIG 2 -12.818 0.276 -2.463 1.00 0.00 H
> HETATM 13 H31 LIG 3 -10.741 1.519 -2.096 1.00 0.00 H
> HETATM 14 H32 LIG 3 -11.953 2.046 -0.903 1.00 0.00 H
> HETATM 15 C1 LIG 3 -9.568 1.894 0.257 1.00 0.00 C
> HETATM 16 C3 LIG 4 -8.673 1.387 1.389 1.00 0.00 C
> HETATM 17 OO2 LIG 4 -7.815 0.358 0.894 1.00 0.00 O
> HETATM 18 H11 LIG 3 -8.949 2.211 -0.582 1.00 0.00 H
> HETATM 19 H12 LIG 3 -10.160 2.738 0.611 1.00 0.00 H
> HETATM 20 H31 LIG 4 -8.070 2.210 1.772 1.00 0.00 H
> HETATM 21 H32 LIG 4 -9.294 0.988 2.192 1.00 0.00 H
> HETATM 22 C1 LIG 4 -6.933 -0.187 1.877 1.00 0.00 C
> HETATM 23 C3 LIG 5 -6.066 -1.274 1.239 1.00 0.00 C
> HETATM 24 OO2 LIG 5 -5.215 -0.687 0.252 1.00 0.00 O
> HETATM 25 H11 LIG 4 -6.294 0.603 2.270 1.00 0.00 H
> HETATM 26 H12 LIG 4 -7.517 -0.619 2.690 1.00 0.00 H
> HETATM 27 H32 LIG 5 -5.457 -1.751 2.007 1.00 0.00 H
> HETATM 28 H31 LIG 5 -6.707 -2.020 0.768 1.00 0.00 H
> HETATM 29 C1 LIG 5 -4.360 -1.621 -0.408 1.00 0.00 C
> HETATM 30 C3 LIG 6 -3.499 -0.885 -1.437 1.00 0.00 C
> HETATM 31 OO2 LIG 6 -2.622 0.020 -0.764 1.00 0.00 O
> HETATM 32 H12 LIG 5 -3.715 -2.105 0.325 1.00 0.00 H
> HETATM 33 H11 LIG 5 -4.965 -2.374 -0.913 1.00 0.00 H
> HETATM 34 H32 LIG 6 -2.910 -1.608 -2.002 1.00 0.00 H
> HETATM 35 H31 LIG 6 -4.143 -0.329 -2.118 1.00 0.00 H
> HETATM 36 C1 LIG 6 -1.769 0.762 -1.639 1.00 0.00 C
> HETATM 37 C3 LIG 7 -0.879 1.694 -0.814 1.00 0.00 C
> HETATM 38 OO2 LIG 7 0.000 0.916 0.000 1.00 0.00 O
> HETATM 39 H12 LIG 6 -1.145 0.073 -2.208 1.00 0.00 H
> HETATM 40 H11 LIG 6 -2.377 1.353 -2.324 1.00 0.00 H
> HETATM 41 H31 LIG 7 -0.293 2.323 -1.484 1.00 0.00 H
> HETATM 42 H32 LIG 7 -1.502 2.323 -0.178 1.00 0.00 H
> HETATM 43 C1 LIG 7 0.879 1.694 0.814 1.00 0.00 C
> HETATM 44 C3 LIG 8 1.769 0.762 1.639 1.00 0.00 C
> HETATM 45 OO2 LIG 8 2.622 0.020 0.764 1.00 0.00 O
> HETATM 46 H11 LIG 7 1.502 2.323 0.178 1.00 0.00 H
> HETATM 47 H12 LIG 7 0.293 2.323 1.484 1.00 0.00 H
> HETATM 48 H32 LIG 8 2.377 1.353 2.324 1.00 0.00 H
> HETATM 49 H31 LIG 8 1.145 0.073 2.208 1.00 0.00 H
> HETATM 50 C1 LIG 8 3.499 -0.885 1.437 1.00 0.00 C
> HETATM 51 C3 LIG 9 4.360 -1.621 0.408 1.00 0.00 C
> HETATM 52 OO2 LIG 9 5.215 -0.687 -0.252 1.00 0.00 O
> HETATM 53 H12 LIG 8 4.143 -0.329 2.118 1.00 0.00 H
> HETATM 54 H11 LIG 8 2.910 -1.608 2.002 1.00 0.00 H
> HETATM 55 H32 LIG 9 4.965 -2.374 0.913 1.00 0.00 H
> HETATM 56 H31 LIG 9 3.715 -2.105 -0.325 1.00 0.00 H
> HETATM 57 C1 LIG 9 6.066 -1.274 -1.239 1.00 0.00 C
> HETATM 58 C3 LIG 10 6.933 -0.187 -1.877 1.00 0.00 C
> HETATM 59 OO2 LIG 10 7.815 0.358 -0.894 1.00 0.00 O
> HETATM 60 H12 LIG 9 6.707 -2.020 -0.768 1.00 0.00 H
> HETATM 61 H11 LIG 9 5.457 -1.751 -2.007 1.00 0.00 H
> HETATM 62 H31 LIG 10 7.517 -0.619 -2.690 1.00 0.00 H
> HETATM 63 H32 LIG 10 6.294 0.603 -2.270 1.00 0.00 H
> HETATM 64 C1 LIG 10 8.673 1.387 -1.389 1.00 0.00 C
> HETATM 65 C3 LIG 11 9.568 1.894 -0.257 1.00 0.00 C
> HETATM 66 OO2 LIG 11 10.441 0.845 0.167 1.00 0.00 O
> HETATM 67 H11 LIG 10 9.294 0.988 -2.192 1.00 0.00 H
> HETATM 68 H12 LIG 10 8.070 2.210 -1.772 1.00 0.00 H
> HETATM 69 H31 LIG 11 10.160 2.738 -0.611 1.00 0.00 H
> HETATM 70 H32 LIG 11 8.949 2.211 0.582 1.00 0.00 H
> HETATM 71 C1 LIG 11 11.325 1.216 1.227 1.00 0.00 C
> HETATM 72 C3 LIG 12 12.207 0.022 1.596 1.00 0.00 C
> HETATM 73 OO2 LIG 12 13.056 -0.302 0.493 1.00 0.00 O
> HETATM 74 H11 LIG 11 11.953 2.046 0.903 1.00 0.00 H
> HETATM 75 H12 LIG 11 10.741 1.519 2.096 1.00 0.00 H
> HETATM 76 H32 LIG 12 12.818 0.276 2.463 1.00 0.00 H
> HETATM 77 H31 LIG 12 11.578 -0.836 1.835 1.00 0.00 H
> HETATM 78 C1 LIG 12 13.927 -1.410 0.735 1.00 0.00 C
> HETATM 79 C3 LIGb 13 14.784 -1.665 -0.506 1.00 0.00 C
> HETATM 80 OO1 LIGb 13 15.647 -0.548 -0.727 1.00 0.00 O
> HETATM 81 H12 LIG 12 14.573 -1.185 1.584 1.00 0.00 H
> HETATM 82 H11 LIG 12 13.333 -2.297 0.956 1.00 0.00 H
> HETATM 83 H32 LIGb 13 15.383 -2.563 -0.355 1.00 0.00 H
> HETATM 84 H31 LIGb 13 14.137 -1.802 -1.372 1.00 0.00 H
> HETATM 85 H11 LIGb 13 16.221 -0.641 -1.500 1.00 0.00 H
> HETATM 86 OO2 LIGe 1 -15.647 -0.548 0.727 1.00 0.00 O
> HETATM 87 H21 LIGe 1 -16.221 -0.641 1.500 1.00 0.00 H
Same as above, but now you're mixing LIGb, LIG, and LIGe in a horrific mess that
pdb2gmx will never be able to sort out :)
-Justin
> TER
> END
>
>
> ********************************************************************************
> snips from pdb2gmx:
>
> WARNING: atom C1 is missing in residue LIGe 1 in the pdb file
>
>
> WARNING: atom H11 is missing in residue LIGe 1 in the pdb file
> You might need to add atom H11 to the hydrogen database of building block LIGe
> in the file merged.hdb (see the manual)
>
>
> WARNING: atom H12 is missing in residue LIGe 1 in the pdb file
> You might need to add atom H12 to the hydrogen database of building block LIGe
> in the file merged.hdb (see the manual)
>
> There were 169 missing atoms in molecule Non-Protein
> Number of bonds was 35, now 24
> Generating angles, dihedrals and pairs...
> Making cmap torsions...There are 0 dihedrals, 0 impropers, 11 angles
> 0 pairs, 24 bonds and 0 virtual sites
> Total mass 546.656 a.m.u.
> Total charge 0.000 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.3#
>
> Writing coordinate file...
>
> Back Off! I just backed up PEG.gro to ./#PEG.gro.3#
> --------- PLEASE NOTE ------------
> You have successfully generated a topology from: PEG_dan2.pdb.
> The Charmm36 force field and the tip3p water model are used.
> --------- ETON ESAELP ------------
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
More information about the gromacs.org_gmx-users
mailing list