[gmx-users] gromacs.org_gmx-users Digest, Vol 120, Issue 32
marzieh dehghan
dehghanmarzieh at gmail.com
Sat Apr 5 21:10:49 CEST 2014
Hi every body
after glycation insulin by autodock, I wan to run it by GROMACS.
I would like to know is it possible and correct?
best regards
thanks a lot
marzieh
On 4/5/14, gromacs.org_gmx-users-request at maillist.sys.kth.se
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: adding metal-bonding parameters to a force field
> (Justin Lemkul)
> 2. Re: adding metal-bonding parameters to a force field
> (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 05 Apr 2014 08:51:47 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] adding metal-bonding parameters to a force
> field
> Message-ID: <533FFC63.70009 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-9; format=flowed
>
>
>
> On 4/5/14, 2:12 AM, Ahmet y?ld?r?m 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 y?ld?r?m 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 y?ld?r?m 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.
>>>
>>
>>
>>
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 05 Apr 2014 08:52:42 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] adding metal-bonding parameters to a force
> field
> Message-ID: <533FFC9A.2020706 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-9; format=flowed
>
>
>
> On 4/5/14, 2:43 AM, Ahmet y?ld?r?m wrote:
>> How will I define ZN(HOH) in aminoacids.hdb?
>>
>
> It's the same as water.
>
> -Justin
>
>>
>> 2014-04-05 9:12 GMT+03:00 Ahmet y?ld?r?m <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 y?ld?r?m 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 y?ld?r?m 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 Y?ld?r?m
>>>
>>
>>
>>
>
> --
> ==================================================
>
> 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
>
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> mail to gmx-users-request at gromacs.org.
>
>
> End of gromacs.org_gmx-users Digest, Vol 120, Issue 32
> ******************************************************
>
--
*Marzieh Dehghan
PhD Candidate of Biochemistry
Institute of biochemistry and Biophysics (IBB)
University of Tehran, Tehran- Iran.*
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