[gmx-users] adding metal-bonding parameters to a force field

Justin Lemkul jalemkul at vt.edu
Sat Apr 5 06:15:29 CEST 2014



On 4/4/14, 11:58 PM, Ahmet yıldırım wrote:
> Hi,
>
> The distance I have set in specbond.dat must correct (req from Table 1). I
> get them from literature.Please see this link:
>
> http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei=GXk_U7XNG7GIyAOMvoBw&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFsPCxQ&sig2=MtbMKLDYZBbb6ACkGJjyMA&bvm=bv.64125504,d.bGQ
>

You've posted this several times.  I understand the source of the parameters. 
The problem is that equilibrium bond lengths and specbond.dat distances are not 
the same.  Please see 
http://www.gromacs.org/Documentation/File_Formats/specbond.dat - if your input 
coordinates do not place the two atoms within 10% of the distance specified in 
specbond.dat, no bond is assigned.  The value in specbond.dat has zero bearing 
on what the bond length should be.

> The His-Zn bonds are correctly generated (req from Table 1). Histidine
> nitrogen atoms (NE2 atoms in His94 and His96, ND1 atom in His119) are bound
> to the Zn+2 ion. In addition Zn is bound to a water molecule.
>
> You said "create a residue that contains Zn(HOH)". Do I need it? I have
> already charge of Zn and each atom of HOH.
>

I think it is more straightforward, but you can approach it however you like.

> I am making these corrections in the right place. I am using Gromacs 4.5.5
> on Ubuntu 12.1. The modified forcefield is in /usr/share/gromacs/top.
>

Well, there's still something wrong, which is weird because the modifications 
are straightforward.  But one thing is true - grompp doesn't throw fatal errors 
for no reason.

> Everything seems normal after pdb2gmx command:
> ..
> Identified residue HIS3 as a starting terminus.
> Identified residue LYS261 as a ending terminus.
> 11 out of 11 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> ....
> Identified residue HIS3 as a starting terminus.
> Identified residue LYS261 as a ending terminus.
> 11 out of 11 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                      HIS3    HIS3    HIS4    HIS4   HIS10   HIS10   HIS15
>                      ND18   NE210   ND118   NE220   ND170   NE273  ND1108
>      HIS3   NE210   0.214
>      HIS4   ND118   0.719   0.694
>      HIS4   NE220   0.882   0.825   0.215
>     HIS10   ND170   1.247   1.294   1.536   1.561
>     HIS10   NE273   1.344   1.361   1.634   1.642   0.212
>     HIS15  ND1108   1.232   1.341   1.321   1.360   0.664   0.858
>     HIS15  NE2111   1.319   1.400   1.400   1.413   0.542   0.711   0.216
>     HIS17  ND1132   1.710   1.859   1.611   1.666   1.483   1.679   0.826
>     HIS17  NE2135   1.651   1.792   1.595   1.643   1.292   1.485   0.645
>     HIS36  ND1288   4.357   4.370   3.902   3.761   3.751   3.787   3.426
>     HIS36  NE2291   4.538   4.546   4.072   3.926   3.940   3.971   3.625
>     HIS64  ND1508   1.631   1.554   0.983   0.777   1.945   1.991   1.718
>     HIS64  NE2514   1.533   1.454   0.855   0.657   1.989   2.043   1.756
>     HIS94  ND1751   2.349   2.275   1.669   1.476   2.593   2.632   2.320
>     HIS94  NE2754   2.302   2.239   1.638   1.446   2.456   2.499   2.168
>     HIS96  ND1772   2.136   2.078   1.563   1.370   2.064   2.093   1.823
>     HIS96  NE2775   2.241   2.188   1.626   1.435   2.244   2.282   1.964
>    HIS107  ND1854   2.863   2.849   2.282   2.122   2.658   2.714   2.285
>    HIS107  NE2857   2.888   2.890   2.310   2.165   2.697   2.769   2.277
>    HIS119  ND1952   2.494   2.449   1.853   1.671   2.516   2.564   2.194
>    HIS119  NE2955   2.656   2.616   2.033   1.854   2.593   2.637   2.267
>    HIS122  ND1977   3.202   3.156   2.492   2.333   3.468   3.531   3.088
>    HIS122  NE2980   3.347   3.290   2.635   2.470   3.620   3.674   3.264
>    CYS206  SG1623   2.512   2.539   1.855   1.775   2.867   2.991   2.343
>    MET241  SD1909   1.925   1.785   1.463   1.255   2.023   1.986   2.036
>                     HIS15   HIS17   HIS17   HIS36   HIS36   HIS64   HIS64
>                    NE2111  ND1132  NE2135  ND1288  NE2291  ND1508  NE2514
>     HIS17  ND1132   0.988
>     HIS17  NE2135   0.794   0.214
>     HIS36  ND1288   3.349   3.219   3.202
>     HIS36  NE2291   3.545   3.426   3.409   0.214
>     HIS64  ND1508   1.712   1.928   1.909   3.206   3.349
>     HIS64  NE2514   1.770   1.953   1.946   3.393   3.537   0.213
>     HIS94  ND1751   2.306   2.383   2.392   2.897   3.008   0.728   0.830
>     HIS94  NE2754   2.148   2.222   2.225   2.724   2.843   0.693   0.835
>     HIS96  ND1772   1.767   1.980   1.941   2.549   2.686   0.692   0.899
>     HIS96  NE2775   1.924   2.048   2.031   2.530   2.660   0.717   0.905
>    HIS107  ND1854   2.246   2.158   2.164   1.771   1.903   1.494   1.665
>    HIS107  NE2857   2.255   2.072   2.095   1.744   1.886   1.582   1.739
>    HIS119  ND1952   2.166   2.184   2.189   2.391   2.511   0.952   1.112
>    HIS119  NE2955   2.229   2.236   2.237   2.178   2.295   1.147   1.317
>    HIS122  ND1977   3.099   2.924   2.986   2.774   2.844   1.669   1.727
>    HIS122  NE2980   3.268   3.128   3.184   2.858   2.914   1.789   1.847
>    CYS206  SG1623   2.425   1.975   2.093   2.940   3.078   1.436   1.431
>    MET241  SD1909   1.953   2.463   2.387   3.327   3.448   0.777   0.894
>                     HIS94   HIS94   HIS96   HIS96  HIS107  HIS107  HIS119
>                    ND1751  NE2754  ND1772  NE2775  ND1854  NE2857  ND1952
>     HIS94  NE2754   0.221
>     HIS96  ND1772   0.694   0.502
>     HIS96  NE2775   0.530   0.317   0.216
>    HIS107  ND1854   1.161   0.977   0.909   0.817
>    HIS107  NE2857   1.274   1.093   1.050   0.950   0.221
>    HIS119  ND1952   0.522   0.337   0.507   0.306   0.642   0.770
>    HIS119  NE2955   0.723   0.549   0.607   0.452   0.452   0.610   0.218
>    HIS122  ND1977   0.995   1.067   1.510   1.296   1.309   1.338   1.033
>    HIS122  NE2980   1.088   1.183   1.629   1.421   1.451   1.499   1.166
>    CYS206  SG1623   1.250   1.213   1.491   1.329   1.390   1.289   1.197
>    MET241  SD1909   1.070   1.062   0.908   1.023   1.787   1.947   1.283
>                    HIS119  HIS122  HIS122  CYS206
>                    NE2955  ND1977  NE2980  SG1623
>    HIS122  ND1977   1.073
>    HIS122  NE2980   1.200   0.219
>    CYS206  SG1623   1.294   1.177   1.388
>    MET241  SD1909   1.421   2.042   2.097   2.143

Note from the above output that no bond is being created between the Zn and any 
His residue.  This is likely a consequence of the chains being processed 
separately.  You likely need to put the Zn(HOH) complex in the same chain as the 
protein, and this is probably another reason for creating a Zn(HOH) residue and 
defining it as protein.  Doing so circumvents all of these quirks.

-Justin

> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
> Checking for duplicate atoms....
> Now there are 2059 atoms. Deleted 21 duplicates.
> Now there are 258 residues with 4071 atoms
> Chain time...
>
> Back Off! I just backed up protein_Protein_chain_A.itp to
> ./#protein_Protein_chain_A.itp.7#
> Making bonds...
> Number of bonds was 4134, now 4133
> Generating angles, dihedrals and pairs...
> Before cleaning: 10879 pairs
> Before cleaning: 11505 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...There are 11505 dihedrals,  834 impropers, 7491
> angles
>            10798 pairs,     4133 bonds and     0 virtual sites
> Total mass 29026.976 a.m.u.
> Total charge -1.000 e
> Writing topology
>
> Back Off! I just backed up posre_Protein_chain_A.itp to
> ./#posre_Protein_chain_A.itp.7#
> Processing chain 2 'A' (2 atoms, 2 residues)
> Warning: Starting residue ZN262 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue OWZ1001 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.
> 11 out of 11 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                     ZN262
>                       ZN1
>   OWZ1001     OZ2   0.188
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
> Checking for duplicate atoms....
> Now there are 2 residues with 4 atoms
> Chain time...
>
> Back Off! I just backed up protein_Ion_chain_A2.itp to
> ./#protein_Ion_chain_A2.itp.7#
> Making bonds...
> Number of bonds was 2, now 2
> Generating angles, dihedrals and pairs...
> Making cmap torsions...There are    0 dihedrals,    0 impropers,    1 angles
>               0 pairs,        2 bonds and     0 virtual sites
> Total mass 83.416 a.m.u.
> Total charge 2.118 e
> Writing topology
>
> Back Off! I just backed up posre_Ion_chain_A2.itp to
> ./#posre_Ion_chain_A2.itp.7#
> Processing chain 3 (310 atoms, 310 residues)
> 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.
> 11 out of 11 lines of specbond.dat converted successfully
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
> Checking for duplicate atoms....
> Now there are 310 residues with 930 atoms
> Making bonds...
> Number of bonds was 620, now 620
> Generating angles, dihedrals and pairs...
> Making cmap torsions...There are    0 dihedrals,    0 impropers,  310 angles
>               0 pairs,      620 bonds and     0 virtual sites
> Total mass 5584.960 a.m.u.
> Total charge 0.000 e
> Including chain 1 in system: 4071 atoms 258 residues
> Including chain 2 in system: 4 atoms 2 residues
> Including chain 3 in system: 930 atoms 310 residues
> Now there are 5005 atoms and 570 residues
> Total mass in system 34695.352 a.m.u.
> Total charge in system 1.118 e
> ..
>
>
>
>
> 2014-04-04 23:28 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 4/4/14, 1:46 PM, Ahmet yıldırım wrote:
>>
>>> Dear Justin,
>>>
>>> These parameters are present in literature. I think these bonds/parameters
>>> are correctly generated. You said "The previous topology output suggests
>>> not, because ZN is not renamed to ZNW".  I do not know what to do.
>>>
>>>
>> Probably because the distance you have set in specbond.dat is incorrect.
>>   I'll ask again - are the His-Zn bonds correctly generated?  If not, that's
>> your problem.  If they are, we'll have to do more digging.  You can avoid
>> the whole Zn-renaming and charge issue if you do as I suggested before and
>> create a residue that contains Zn(HOH), not just ZN and then a separate
>> residue for the water bound to it.  Treat it as its own entity.
>>
>>
>>   I added the OZ-HZ bond in ffbonded.itp. Unfortunately I get the same
>>> errors:
>>>
>>> ERROR 1 [file protein_Ion_chain_A2.itp, line 33]:
>>>     No default Bond types
>>> ERROR 2 [file protein_Ion_chain_A2.itp, line 34]:
>>>     No default Bond types
>>>
>>> ffbonded.itp:
>>>     Zn NA         1    0.20500   16744.0 ;modified
>>>     Zn NB         1    0.20500   16744.0 ;modified
>>>     Zn OZ         1    0.23000   16744.0 ;modified
>>>     OZ HZ         1    0.09572   221682.2 ;modified
>>>
>>>
>> Are you making these corrections in the right place?  Does your .top call
>> your modified force field?  Are you modifying files in $GMXLIB or in the
>> working directory?
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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