[gmx-users] adding metal-bonding parameters to a force field
Ahmet yıldırım
ahmedo047 at gmail.com
Sat Apr 5 08:12:12 CEST 2014
You said "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".
How will I do what you say?
2014-04-05 7:13 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
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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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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>
--
Ahmet Yıldırım
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