[gmx-users] adding metal-bonding parameters to a force field
Justin Lemkul
jalemkul at vt.edu
Sat Apr 5 14:53:28 CEST 2014
On 4/5/14, 2:12 AM, Ahmet yıldırım wrote:
> 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?
>
Assuming you have a .pdb file, just give it the same chain identifier.
-Justin
>
> 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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>>>> 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 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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>> 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 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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