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 <jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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