[gmx-users] first residue in chains warning issue
Ming Tang
m21.tang at qut.edu.au
Mon May 18 13:39:19 CEST 2015
Dear Justin,
After minimization, I got the following note when using NPT.
NOTE 1 [file topol.top, line 49]:
The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10
times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option.
Does this has something to do with the warning given by pdb2gmx?
When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there anything wrong with my topol.top?
Thanks.
-----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: Tuesday, 12 May 2015 10:19 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue
On 5/12/15 8:10 AM, Ming Tang wrote:
>
> Thanks Justin,
>
> At first, I wanted to choose NONE in for both N and C terminus, but it gave me the same warnings for both the first and the last residue in every chains. However, choose NH3+/COO- and NH2/COOH just gave that warning for the first residue.
>
Right, because choosing "None" is chemical nonsense in this context.
> The angles and bonds in .itp are like this:
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 2 gb_2
> 1 3 2 gb_2
> 1 4 2 gb_21
> 4 5 2 gb_27
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 3 2 ga_10
> 2 1 4 2 ga_10
> 2 1 5 2 ga_11
> 3 1 4 2 ga_10
> 3 1 5 2 ga_11
> 4 1 5 2 ga_11
> 1 5 6 2 ga_13
> 1 5 13 2 ga_13
> 6 5 13 2 ga_13
>
> Just now, I tried to delete one H atom of the first residue in the input .pdb, but got the same warnings for them. Is there anything wrong with the angle and bond?
Well, cross-reference what the atoms are and what the parameters should be.
That's your job, not mine :) Energy minimization and a quick MD run will show you if there are any problems; if things are missing or wrong (very unlikely, but always check when you see warnings!) then the structure will be obviously wrong very quickly. Like I said, this is really most likely just some weird case in the code that isn't handled elegantly, but there's not enough to go on for a full debug.
-Justin
> -----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: Tuesday, 12 May 2015 9:35 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] first residue in chains warning issue
>
>
>
> On 5/11/15 6:48 PM, Ming Tang wrote:
>> 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
>
> Any reason for these selections? There exists no pH value at which the N-terminus is NH2 and the C-terminus is COOH, unless you have some very strange microenvironments that cause pKa shifts.
>
>> 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.
>>
>
> Yes, that's correct, per your terminus selection.
>
>> 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?
>
> The salient parts of the topology are the bonds and angles (because
> the warning came about an angle), so check and make sure everything is
> right for the bonds and angles involving N-H[12]. I suspect something
> funky is going on because of your input file having three of the same
> (H) atoms; these should, in principle, be ignored with -ignh, but who
> knows what happens when you're trying to run something atypical
> through the ugly guts of pdb2gmx :)
>
> -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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--
==================================================
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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