[gmx-users] Too many error at first step

Mon Jan 30 17:54:33 CET 2017

Hello Justin,

Which force field should I use?
Further, How to check the compatibility of protein for force field? PDB id
of my protein is 4g7a.
Secondly, I am using Gromacs VERSION 5.1.4 which is most updated.

Thanking you,
Chinatn

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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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-- 
Regards,
Chintan Bhagat
Mob. +91 88 66 61 11 49