[gmx-users] first residue in chains warning issue

Ming Tang m21.tang at qut.edu.au
Tue May 12 14:55:57 CEST 2015


Thanks. EM and NPT run without any warnings.

Sent from my Huawei Mobile

Justin Lemkul <jalemkul at vt.edu> wrote:



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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