[gmx-users] Too many error at first step

[Mark Abraham]

Hi,

You chose a force field capable of describing the protein + Mg ion. Well
done. Whether that will be a good model of physics of your system remains
to be seen. I would strongly suggest finding a different problem for your
first MD study. There are far too many errors to make without needing to
deal with doubtful metal parameters, or modified ligands. Learn to walk
before trying to run juggling knives!

Mark

On Wed, Feb 15, 2017 at 2:25 PM Chintan Bhagat <cbb.chintan at gmail.com>
wrote:

> Dear Justin,
>
> Thank you for your reply.
>
> I selected my protein for MD study and I did the stimulation same as
> mentioned in  lysozyme tutorial *using force field - GROMOS96 43a1 force
> field *(As, I came to know all force field has different .mdp file, so
> results are not vaild). I did the same as mention in tutorial (using .mdp
> fie). But, When i selected  OPLS-AA/L all-atom force field, I got error
> message,* Residue 'ZN' not found in residue topology database*.
>
> Later, I search on literature, I found chaining ZN to MG is good and will
> does not make any significance changes in result. So, I replaced ZN by MG
> in my file and run the stimulation using OPLS-AA/L all-atom force field (
>
> https://www.researchgate.net/post/How_can_I_rectify_this_error_Atom_type_Zn2_residue_ZN_not_found_in_atomtype_database
> ).
> This time, I did not got any error or warning message. As, I  am new, I am
> not sure, I am doing right or not .
>
> I also search for for adding residue to force field file, but not able do
> well (
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> ).
>
>
> I request you to suggest me whether I am doing right or not? (As, I am not
> expert!!!!!!)
>
> hope you reply.
>
> On Mon, Jan 30, 2017 at 10:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 1/30/17 11:54 AM, Chintan Bhagat wrote:
> >
> >> Hello Justin,
> >>
> >> Which force field should I use?
> >>
> >
> > One that supports what you need.  I don't mean that to be dismissive;
> it's
> > your job in designing your research to look at the pros and cons of each
> > force field, and no one can or should make that (very critical) decision
> > for you.  Has it been demonstrated to be effective for similar systems?
> > What are the limitations?
> >
> > Further, How to check the compatibility of protein for force field? PDB
> id
> >> of my protein is 4g7a.
> >>
> >
> > The protein isn't the issue.  Every force field in GROMACS will handle
> the
> > protein.  But Zn is another matter.  This again requires an investigation
> > and assessment of the literature.
> >
> > Secondly, I am using Gromacs VERSION 5.1.4 which is most updated.
> >>
> >>
> > No, version 2016.1 is the latest, and I personally fixed the bug I
> > referred to for this version after 5.1.4 was released.  Trust me, I'm
> > trying to help you avoid a very serious serious bug :)
> >
> > -Justin
> >
> > Thanking you,
> >> Chinatn
> >>
> >>
> >>
> >>   <https://mailtrack.io/>Sent with Mailtrack
> >> <https://mailtrack.io/install?source=signature&lang=en&refer
> >> ral=cbb.chintan at gmail.com&idSignature=22>
> >>
> >>
> >> On Mon, Jan 30, 2017 at 9:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 1/30/17 11:08 AM, Chintan Bhagat wrote:
> >>>
> >>> Hello all,
> >>>>
> >>>> I am new to Gromacs, and I completed the Lysozyme tutorial. But When I
> >>>> started stimulation with my own protein, I got many errors. I am not
> >>>> understanding what to do?
> >>>>
> >>>> For error
> >>>> ------------------------------------------------------------
> >>>> ---------------------------------------------------------
> >>>>
> >>>> lab at lab-desktop:~/Desktop/MD_tutorial$ gmx pdb2gmx -f 4g7a.pdb -o
> >>>> 4g7a_processed.gro -water spce
> >>>> .
> >>>> .
> >>>> .
> >>>> .
> >>>> .
> >>>> ........
> >>>> gmx pdb2gmx -f 4g7a.pdb -o 4g7a_processed.gro -water spce
> >>>>
> >>>>
> >>>> Select the Force Field:
> >>>> From '/usr/local/gromacs/share/gromacs/top':
> >>>> 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
> >>>> 1999-2012, 2003)
> >>>> 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> >>>> 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res.
> 29,
> >>>> 461-469, 1996)
> >>>> 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
> >>>> 1049-1074, 2000)
> >>>> 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
> >>>> 712-725,
> >>>> 2006)
> >>>> 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
> >>>> Proteins 78, 1950-58, 2010)
> >>>> 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787,
> 2002)
> >>>> 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> >>>> 9: GROMOS96 43a1 force field
> >>>> 10: GROMOS96 43a2 force field (improved alkane dihedrals)
> >>>> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> >>>> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> >>>> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> >>>> 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856,
> >>>> DOI:
> >>>> 10.1007/s00249-011-0700-9)
> >>>> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> >>>> 15
> >>>>
> >>>> Using the Oplsaa force field in directory oplsaa.ff
> >>>>
> >>>> Opening force field file
> >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
> >>>> Reading 4g7a.pdb...
> >>>>
> >>>> *WARNING: all CONECT records are ignored*
> >>>> Read 'CARBONATE DEHYDRATASE', 3726 atoms
> >>>> Analyzing pdb file
> >>>> Splitting chemical chains based on TER records or chain id changing.
> >>>>
> >>>> *WARNING: Chain identifier 'A' is used in two non-sequential blocks*.
> >>>> They will be treated as separate chains unless you reorder your file.
> >>>>
> >>>> *WARNING: Chain identifier 'B' is used in two non-sequential blocks.*
> >>>> They will be treated as separate chains unless you reorder your file.
> >>>> There are 4 chains and 0 blocks of water and 453 residues with 3726
> >>>> atoms
> >>>>
> >>>> chain #res <https://plus.google.com/u/0/s/%23res> #atoms
> >>>> <https://plus.google.com/u/0/s/%23atoms>
> >>>> 1 'A' 224 1850
> >>>> 2 'B' 225 1848
> >>>> 3 'A' 2 14
> >>>> 4 'B' 2 14
> >>>>
> >>>>
> >>>>
> >>>> *WARNING: there were 0 atoms with zero occupancy and 24 atoms
> >>>> withoccupancy
> >>>> unequal to one (out of 3726 atoms). Check your pdb file.*
> >>>>
> >>>>
> >>>> Opening force field file
> >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
> >>>> Atomtype 814
> >>>> Reading residue database... (oplsaa)
> >>>> Opening force field file
> >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
> >>>> Residue 51
> >>>> Sorting it all out...
> >>>> Opening force field file
> >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
> >>>> Opening force field file
> >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
> >>>> Opening force field file
> >>>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
> >>>> Processing chain 1 'A' (1850 atoms, 224 residues)
> >>>> Analysing hydrogen-bonding network for automated assignment of
> histidine
> >>>> protonation. 348 donors and 340 acceptors were found.
> >>>> There are 571 hydrogen bonds
> >>>> Will use HISE for residue 13
> >>>> Will use HISE for residue 64
> >>>> Will use HISD for residue 89
> >>>> Will use HISD for residue 91
> >>>> Will use HISH for residue 96
> >>>> Will use HISE for residue 108
> >>>> Will use HISE for residue 111
> >>>> Identified residue GLU2 as a starting terminus.
> >>>> Identified residue PHE225 as a ending terminus.
> >>>> 8 out of 8 lines of specbond.dat converted successfully
> >>>> Special Atom Distance matrix:
> >>>> HIS13 CYS24 HIS64 HIS89 HIS91 HIS96 HIS108
> >>>> NE2102 SG205 NE2537 NE2752 NE2773 NE2812 NE2920
> >>>> CYS24 SG205 1.292
> >>>> HIS64 NE2537 1.662 1.215
> >>>> HIS89 NE2752 2.291 1.422 1.134
> >>>> HIS91 NE2773 2.078 1.340 1.109 0.319
> >>>> HIS96 NE2812 2.309 1.478 1.921 1.078 0.956
> >>>> HIS108 NE2920 2.341 1.518 1.551 0.549 0.461 0.594
> >>>> HIS111 NE2948 3.366 2.266 2.218 1.186 1.430 1.481 1.207
> >>>> MET124 SD1042 2.668 2.087 2.115 1.201 1.040 0.821 0.722
> >>>> MET167 SD1384 3.105 2.374 2.793 1.822 1.730 0.920 1.288
> >>>> CYS178 SG1462 1.405 0.204 1.183 1.243 1.160 1.286 1.317
> >>>> MET205 SD1680 2.313 1.909 1.145 0.868 0.772 1.646 1.112
> >>>> HIS111 MET124 MET167 CYS178
> >>>> NE2948 SD1042 SD1384 SG1462
> >>>> MET124 SD1042 1.600
> >>>> MET167 SD1384 1.756 0.956
> >>>> CYS178 SG1462 2.083 1.895 2.189
> >>>> MET205 SD1680 1.859 1.368 2.264 1.770
> >>>> Linking CYS-24 SG-205 and CYS-178 SG-1462...
> >>>> Start terminus GLU-2: NH3+
> >>>> End terminus PHE-225: COO-
> >>>> Checking for duplicate atoms....
> >>>> Now there are 1838 atoms. Deleted 12 duplicates.
> >>>> Generating any missing hydrogen atoms and/or adding termini.
> >>>> Now there are 224 residues with 3714 atoms
> >>>> Chain time...
> >>>> Making bonds...
> >>>> Number of bonds was 3759, now 3759
> >>>> Generating angles, dihedrals and pairs...
> >>>> Before cleaning: 9973 pairs
> >>>> Before cleaning: 10098 dihedrals
> >>>> Keeping all generated dihedrals
> >>>> Making cmap torsions...
> >>>> There are 10098 dihedrals, 698 impropers, 6858 angles
> >>>> 9913 pairs, 3759 bonds and 0 virtual sites
> >>>> Total mass 26036.211 a.m.u.
> >>>> Total charge 8.548 e
> >>>> Writing topology
> >>>> Processing chain 2 'B' (1848 atoms, 225 residues)
> >>>> Analysing hydrogen-bonding network for automated assignment of
> histidine
> >>>> protonation. 347 donors and 337 acceptors were found.
> >>>> There are 552 hydrogen bonds
> >>>> Will use HISE for residue 1
> >>>> Will use HISE for residue 13
> >>>> Will use HISE for residue 64
> >>>> Will use HISD for residue 89
> >>>> Will use HISD for residue 91
> >>>> Will use HISH for residue 96
> >>>> Will use HISE for residue 108
> >>>> Will use HISH for residue 111
> >>>> Identified residue HIS1 as a starting terminus.
> >>>> Identified residue PHE225 as a ending terminus.
> >>>> 8 out of 8 lines of specbond.dat converted successfully
> >>>> Special Atom Distance matrix:
> >>>> HIS1 HIS13 CYS24 HIS64 HIS89 HIS91 HIS96
> >>>> NE210 NE2112 SG215 NE2541 NE2756 NE2777 NE2816
> >>>> HIS13 NE2112 1.745
> >>>> CYS24 SG215 1.666 1.257
> >>>> HIS64 NE2541 0.500 1.577 1.214
> >>>> HIS89 NE2756 1.514 2.190 1.415 1.130
> >>>> HIS91 NE2777 1.489 1.982 1.344 1.115 0.315
> >>>> HIS96 NE2816 2.357 2.227 1.484 1.924 1.081 0.956
> >>>> HIS108 NE2918 1.946 2.252 1.526 1.555 0.551 0.459 0.601
> >>>> HIS111 NE2946 2.566 3.262 2.242 2.196 1.172 1.412 1.483
> >>>> MET124 SD1040 2.434 2.585 2.097 2.116 1.194 1.033 0.823
> >>>> MET167 SD1382 3.228 3.066 2.419 2.830 1.853 1.758 0.958
> >>>> CYS178 SG1460 1.659 1.358 0.203 1.185 1.238 1.166 1.291
> >>>> MET205 SD1678 1.254 2.207 1.915 1.146 0.874 0.778 1.653
> >>>> HIS108 HIS111 MET124 MET167 CYS178
> >>>> NE2918 NE2946 SD1040 SD1382 SG1460
> >>>> HIS111 NE2946 1.196
> >>>> MET124 SD1040 0.711 1.581
> >>>> MET167 SD1382 1.317 1.779 0.974
> >>>> CYS178 SG1460 1.326 2.060 1.905 2.233
> >>>> MET205 SD1678 1.116 1.849 1.369 2.293 1.779
> >>>> Linking CYS-24 SG-215 and CYS-178 SG-1460...
> >>>> Start terminus HIS-1: NH3+
> >>>> End terminus PHE-225: COO-
> >>>> Checking for duplicate atoms....
> >>>> Generating any missing hydrogen atoms and/or adding termini.
> >>>> Now there are 225 residues with 3732 atoms
> >>>> Chain time...
> >>>> Making bonds...
> >>>> Number of bonds was 3778, now 3778
> >>>> Generating angles, dihedrals and pairs...
> >>>> Before cleaning: 10019 pairs
> >>>> Before cleaning: 10149 dihedrals
> >>>> Keeping all generated dihedrals
> >>>> Making cmap torsions...
> >>>> There are 10149 dihedrals, 705 impropers, 6891 angles
> >>>> 9959 pairs, 3778 bonds and 0 virtual sites
> >>>> Total mass 26174.361 a.m.u.
> >>>> Total charge 9.548 e
> >>>> Writing topology
> >>>> Processing chain 3 'A' (14 atoms, 2 residues)
> >>>> Warning: Starting residue ZN301 in chain not identified as
> >>>> Protein/RNA/DNA.
> >>>> Warning: Starting residue AZM302 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
> >>>>
> >>>> -------------------------------------------------------
> >>>> Program gmx pdb2gmx, VERSION 5.1.4
> >>>> Source code file:
> >>>> /home/lab/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c, line: 645
> >>>>
> >>>>
> >>>> *Fatal error:Residue 'ZN' not found in residue topology database*
> >>>> For more information and tips for troubleshooting, please check the
> >>>> GROMACS
> >>>> website at http://www.gromacs.org/Documentation/Errors
> >>>> -------------------------------------------------------
> >>>>
> >>>> lab at lab-desktop:~/Desktop/MD_tutorial$
> >>>>
> >>>>
> >>>> OPLS-AA does not support Zn ions.  You'll need to either import
> >>> parameters
> >>> from the literature (if they exist) or use a force field that does
> >>> support
> >>> it.
> >>>
> >>> The more immediate concern is the fractional charges on the chains.
> >>> There
> >>> was a bug that was fixed some time ago regarding incorrect histidine
> >>> charges.  Please upgrade immediately to version 2016.1 if you want to
> use
> >>> OPLS-AA so you get correct files.  The topology you're currently
> >>> producing
> >>> is incorrect.
> >>>
> >>> -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
> >>>
> >>> ==================================================
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at http://www.gromacs.org/Support
> >>> /Mailing_Lists/GMX-Users_List before posting!
> >>>
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> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >>>
> >>
> >>
> >>
> > --
> > ==================================================
> >
> > 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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
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> >
>
>
>
> --
> Regards,
> Chintan Bhagat
> Research scholar,
> Veer Narmad South Gujarat University,
> India
> --
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