[gmx-users] adding metal-bonding parameters to a force field
Ahmet yıldırım
ahmedo047 at gmail.com
Sat Apr 5 08:43:45 CEST 2014
How will I define ZN(HOH) in aminoacids.hdb?
2014-04-05 9:12 GMT+03:00 Ahmet yıldırım <ahmedo047 at gmail.com>:
> 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!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> 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
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> Ahmet Yıldırım
>
--
Ahmet Yıldırım
More information about the gromacs.org_gmx-users
mailing list