[gmx-users] first residue in chains warning issue
Ming Tang
m21.tang at qut.edu.au
Tue May 12 00:48:20 CEST 2015
Hi Justin,
Here is the output of pdb2gmx:
Command line:
pdb2gmx -f hyp_lys.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC
Using the Gromos54a7 force field in directory gromos54a7.ff
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
Reading hyp_lys.pdb...
Read 20130 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 3 chains and 0 blocks of water and 3134 residues with 20130 atoms
chain #res #atoms
1 'A' 1054 6788
2 'B' 1026 6554
3 'C' 1054 6788
All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
Atomtype 58
Reading residue database... (gromos54a7)
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper dihedral
Residue 108
Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 'A' (6788 atoms, 1054 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 1365 donors and 1444 acceptors were found.
There are 1748 hydrogen bonds
Will use HISE for residue 105
Will use HISE for residue 948
Identified residue GLN1 as a starting terminus.
Identified residue TYR1054 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET2 MET19 MET55 MET102 HIS105 MET139 MET418
SD15 SD136 SD369 SD678 NE2702 SD926 SD2692
MET19 SD136 5.356
MET55 SD369 16.259 10.913
MET102 SD678 29.737 24.390 13.588
HIS105 NE2702 30.104 24.755 13.935 0.427
MET139 SD926 40.534 35.194 24.356 10.855 10.499
MET418 SD2692 121.526 116.225 105.475 91.946 91.605 81.150
MET567 SD3648 163.789 158.490 147.754 134.205 133.865 123.429 42.327
MET838 SD5366 241.858 236.550 225.799 212.233 211.888 201.460 120.429
HIS948 NE26069 273.040 267.735 256.991 243.424 243.081 232.655 151.608
MET567 MET838
SD3648 SD5366
MET838 SD5366 78.135
HIS948 NE26069 109.299 31.201
Select start terminus type for GLN-1
0: NH3+
1: NH2
2: None
1
Start terminus GLN-1: NH2
Select end terminus type for TYR-1054
0: COO-
1: COOH
2: None
1
End terminus TYR-1054: COOH
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1054 residues with 8346 atoms
Chain time...
Back Off! I just backed up topol_Protein_chain_A.itp to ./#topol_Protein_chain_A.itp.2#
Making bonds...
Number of bonds was 8606, now 8602
Generating angles, dihedrals and pairs...
WARNING: WARNING: Residue 1 named GLN of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
Before cleaning: 14519 pairs
Before cleaning: 16187 dihedrals
Making cmap torsions...
There are 5421 dihedrals, 3614 impropers, 12466 angles
14519 pairs, 8602 bonds and 0 virtual sites
Total mass 96375.038 a.m.u.
Total charge 8.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_A.itp to ./#posre_Protein_chain_A.itp.2#
Processing chain 2 'B' (6554 atoms, 1026 residues)
I checked the output complex.gro and topol_Protein_Chain_A.itp, and found that the first GLN has only one H atom more than other GLN, which I think is correct.
1GLN N 1 -1.055 1.642 -0.003
1GLN H1 2 -1.105 1.722 -0.036
1GLN H2 3 -0.979 1.623 -0.064
1GLN CA 4 -1.008 1.667 0.124
1GLN CB 5 -1.122 1.705 0.221
1GLN CG 6 -1.078 1.745 0.361
1GLN CD 7 -1.194 1.789 0.448
1GLN OE1 8 -1.309 1.791 0.404
1GLN NE2 9 -1.164 1.827 0.572
1GLN HE21 10 -1.069 1.824 0.603
1GLN HE22 11 -1.237 1.857 0.634
1GLN C 12 -0.930 1.549 0.184
1GLN O 13 -0.964 1.434 0.161
40GLN N 334 0.845 1.381 11.647
40GLN H 335 0.761 1.434 11.633
40GLN CA 336 0.932 1.413 11.759
40GLN CB 337 0.862 1.510 11.855
40GLN CG 338 0.950 1.559 11.969
40GLN CD 339 0.879 1.660 12.057
40GLN OE1 340 0.759 1.684 12.043
40GLN NE2 341 0.953 1.720 12.150
40GLN HE21 342 1.051 1.697 12.158
40GLN HE22 343 0.912 1.787 12.211
40GLN C 344 0.979 1.290 11.834
40GLN O 345 0.897 1.214 11.885
; residue 1 GLN rtp GLN q 0.0
1 NL 1 GLN N 1 -0.66 14.0067 ; qtot -0.66
2 H 1 GLN H1 1 0.44 1.008 ; qtot -0.22
3 H 1 GLN H2 1 0.44 1.008 ; qtot 0.22
4 CH1 1 GLN CA 2 -0.22 13.019 ; qtot 0
5 CH2 1 GLN CB 2 0 14.027 ; qtot 0
6 CH2 1 GLN CG 2 0 14.027 ; qtot 0
7 C 1 GLN CD 3 0.29 12.011 ; qtot 0.29
8 O 1 GLN OE1 3 -0.45 15.9994 ; qtot -0.16
9 NT 1 GLN NE2 3 -0.72 14.0067 ; qtot -0.88
10 H 1 GLN HE21 3 0.44 1.008 ; qtot -0.44
11 H 1 GLN HE22 3 0.44 1.008 ; qtot 0
12 C 1 GLN C 4 0.45 12.011 ; qtot 0.45
13 O 1 GLN O 4 -0.45 15.9994 ; qtot 0
; residue 40 GLN rtp GLN q 0.0
334 N 40 GLN N 159 -0.31 14.0067 ; qtot -0.31
335 H 40 GLN H 159 0.31 1.008 ; qtot 0
336 CH1 40 GLN CA 160 0 13.019 ; qtot 0
337 CH2 40 GLN CB 160 0 14.027 ; qtot 0
338 CH2 40 GLN CG 160 0 14.027 ; qtot 0
339 C 40 GLN CD 161 0.29 12.011 ; qtot 0.29
340 O 40 GLN OE1 161 -0.45 15.9994 ; qtot -0.16
341 NT 40 GLN NE2 161 -0.72 14.0067 ; qtot -0.88
342 H 40 GLN HE21 161 0.44 1.008 ; qtot -0.44
343 H 40 GLN HE22 161 0.44 1.008 ; qtot 0
344 C 40 GLN C 162 0.45 12.011 ; qtot 0.45
345 O 40 GLN O 162 -0.45 15.9994 ; qtot 0
But it does not give any warnings about the last residue of the three chains. Is there anything wrong with this .itp?
Thanks a lot.
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Monday, 11 May 2015 9:44 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue
On 5/10/15 11:36 PM, Ming Tang wrote:
> Dear all,
>
> I built a triple helix with 2 GLN and 1 SER being the first residue of the three chains. However, while using pdb2gmx -f 1.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC and choosing NH2 or NH3+ as the start terminus type for GLN-1 and SER-1, I came across the following warnings:
>
> WARNING: WARNING: Residue 1 named GLN (SER) of a molecule in the input
> file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.
>
You'll need to provide the full screen output from pdb2gmx; this shouldn't happen if all the selections are made correctly and chain termini are identified as they should be.
> Then, I checked the .pdb and .rtp files. The difference between GLN-1/SER-1 and GLN-n/SER-n (n>1) is that GLN-1/SER-1 contains 2 more H atoms.
>
Because you're providing a fully protonated N-terminus (which is fine) with non-unique atom names (which pdb2gmx will take care of when using -ignh).
> Residue GLN-1 in .pdb
> ATOM 1 N GLN A 1 -10.554 16.421 -0.030 1.00 0.00 N1+
> ATOM 2 CA GLN A 1 -10.080 16.667 1.238 1.00 0.00 C
> ATOM 3 C GLN A 1 -9.305 15.495 1.835 1.00 0.00 C
> ATOM 4 O GLN A 1 -9.636 14.335 1.608 1.00 0.00 O
> ATOM 5 CB GLN A 1 -11.222 17.053 2.210 1.00 0.00 C
> ATOM 6 CD GLN A 1 -11.943 17.895 4.480 1.00 0.00 C
> ATOM 7 NE2 GLN A 1 -11.643 18.268 5.719 1.00 0.00 N
> ATOM 8 OE1 GLN A 1 -13.093 17.905 4.041 1.00 0.00 O
> ATOM 9 CG GLN A 1 -10.784 17.445 3.612 1.00 0.00 C
> ATOM 10 HE2 GLN A 1 -12.366 18.573 6.339 1.00 0.00 H
> ATOM 11 HE2 GLN A 1 -10.694 18.243 6.032 1.00 0.00 H
> ATOM 12 H GLN A 1 -11.086 17.245 -0.422 1.00 0.00 H
> ATOM 13 H GLN A 1 -9.773 16.207 -0.708 1.00 0.00 H
> ATOM 14 H GLN A 1 -11.212 15.593 -0.048 1.00 0.00 H
>
> Parameters in .rtp in gromos54a7
> [ GLN ]
> [ atoms ]
> N N -0.31000 0
> H H 0.31000 0
> CA CH1 0.00000 1
> CB CH2 0.00000 1
> CG CH2 0.00000 1
> CD C 0.29000 2
> OE1 O -0.45000 2
> NE2 NT -0.72000 2
> HE21 H 0.44000 2
> HE22 H 0.44000 2
> C C 0.450 3
> O O -0.450 3
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_32
> -C N CA ga_31
> H N CA ga_18
> N CA CB ga_13
> N CA C ga_13
> CB CA C ga_13
> CA CB CG ga_15
> CB CG CD ga_15
> CG CD OE1 ga_30
> CG CD NE2 ga_19
> OE1 CD NE2 ga_33
> CD NE2 HE21 ga_23
> CD NE2 HE22 ga_23
> HE21 NE2 HE22 ga_24
> CA C O ga_30
> CA C +N ga_19
> O C +N ga_33
>
> Further, I compared atoms of GLN in .pdb and .rtp, and changed 2 HE into HE21 and HE22, but got the same warnings.
>
You're using -ignh, so all H atoms are ignored per your instruction.
> The simulation can be move forward to EM and NPT smoothly. Does this kind of warning affect the simulation results significantly?
>
If the topology winds up being sane, then it's fine, but warnings from pdb2gmx are usually weird in the case of normal topologies. Inspect the termini.
-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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