[gmx-users] Too many error at first step

Tue Feb 28 11:42:34 CET 2017

Dear Justin,

I updated Gromacs to 2016.2 but still, I am getting the same problem. I got
following errors.

1. WARNING: all CONECT records are ignored

2. 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 454 residues with 3907 atoms

3. WARNING: there were 0 atoms with zero occupancy and 556 atoms with
         occupancy unequal to one (out of 3907 atoms). Check your pdb file.

I hope you can help me.

Thanking You
Chintan

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
>>>
>>> ==================================================
>>> --
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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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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>
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>

-- 
Regards,
Chintan Bhagat
Research scholar,
Veer Narmad South Gujarat University,
India