mail-vtanchuk wrote:
Dear GMX'ers,
Is there any reliable way of making an itp file for an arbitrary
structure? AFAIK there are two ways:
1) The Dundee PRODRG server. This is really a nice tool, but it
always gives the same protonation states. COOH always becomes COO- and
NH2 becomes NH3+.
You can control the protonation state. See the PRODRG FAQ.
2) x2top. This utility hangs with my rather simple structure.
The structure is attached below. This is a file created by SwissPDB. It
contains hydrogens and connections. Nevertheless x2top ignores this
information and hanges (at least gives no result in 40 min).
It depends on the version of x2top you're using, but if you use the -nopbc
option with version 4.0.5, it doesn't hang.
Otherwise, there are a number of topology-generating tools on the User
Contributions section of the Gromacs site.
-Justin
So, the question is how to make an itp file with predefined protonation
(e.g. COOH and NH2 groups).
Here is a pdb file
COMPND ?
REMARK File generated by Swiss-PdbViewer 3.70b15
REMARK http://www.expasy.org/spdbv/
HETATM 1 C1 PDR 1 43.433 46.174 18.374 1.00 0.00
HETATM 2 C2 PDR 1 42.232 46.505 18.873 1.00 0.00
HETATM 3 C3 PDR 1 41.148 45.500 19.008 1.00 0.00
HETATM 4 C4 PDR 1 41.322 44.220 18.637 1.00 0.00
HETATM 5 C5 PDR 1 43.713 44.783 17.941 1.00 0.00
HETATM 6 C6 PDR 1 42.617 43.776 18.072 1.00 0.00
HETATM 7 C7 PDR 1 42.814 42.509 17.658 1.00 0.00
HETATM 8 C8 PDR 1 44.112 42.120 17.056 1.00 0.00
HETATM 9 C9 PDR 1 45.096 43.026 16.934 1.00 0.00
HETATM 10 C10 PDR 1 44.906 44.416 17.421 1.00 0.00
HETATM 11 O11 PDR 1 45.923 45.378 17.183 1.00 0.00
HETATM 12 C12 PDR 1 46.990 45.244 18.162 1.00 0.00
HETATM 13 C13 PDR 1 48.059 46.309 17.874 1.00 0.00
HETATM 14 O14 PDR 1 47.658 47.553 18.487 1.00 0.00
HETATM 15 C15 PDR 1 49.462 45.937 18.365 1.00 0.00
HETATM 16 N16 PDR 1 50.433 46.887 17.760 1.00 0.00
HETATM 17 C17 PDR 1 51.853 46.544 17.977 1.00 0.00
HETATM 18 C18 PDR 1 52.609 47.864 18.047 1.00 0.00
HETATM 19 C19 PDR 1 52.323 45.695 16.799 1.00 0.00
HETATM 20 H20 PDR 1 44.210 46.934 18.283 1.00 0.00
HETATM 21 H21 PDR 1 42.045 47.532 19.182 1.00 0.00
HETATM 22 H22 PDR 1 40.189 45.815 19.415 1.00 0.00
HETATM 23 H23 PDR 1 40.502 43.512 18.747 1.00 0.00
HETATM 24 H24 PDR 1 42.022 41.768 17.745 1.00 0.00
HETATM 25 H25 PDR 1 44.262 41.102 16.703 1.00 0.00
HETATM 26 H26 PDR 1 46.043 42.752 16.477 1.00 0.00
HETATM 27 H27 PDR 1 46.604 45.386 19.200 1.00 0.00
HETATM 28 H28 PDR 1 47.445 44.230 18.086 1.00 0.00
HETATM 29 H29 PDR 1 48.112 46.449 16.767 1.00 0.00
HETATM 30 H30 PDR 1 46.667 47.789 18.307 1.00 0.00
HETATM 31 H31 PDR 1 49.482 46.012 19.479 1.00 0.00
HETATM 32 H32 PDR 1 49.703 44.893 18.063 1.00 0.00
HETATM 33 H33 PDR 1 50.059 47.894 17.760 1.00 0.00
HETATM 34 H34 PDR 1 52.006 45.989 18.938 1.00 0.00
HETATM 35 H35 PDR 1 52.229 48.461 18.906 1.00 0.00
HETATM 36 H36 PDR 1 53.699 47.688 18.188 1.00 0.00
HETATM 37 H37 PDR 1 52.451 48.451 17.115 1.00 0.00
HETATM 38 H38 PDR 1 51.808 44.708 16.822 1.00 0.00
HETATM 39 H39 PDR 1 52.067 46.197 15.838 1.00 0.00
HETATM 40 H40 PDR 1 53.421 45.523 16.846 1.00 0.00
CONECT 1 2 5 20
CONECT 2 3 21
CONECT 3 4 22
CONECT 4 6 23
CONECT 5 6 10
CONECT 6 7
CONECT 7 8 24
CONECT 8 9 25
CONECT 9 10 26
CONECT 10 11
CONECT 11 12
CONECT 12 13 27 28
CONECT 13 14 15 29
CONECT 14 30
CONECT 15 16 31 32
CONECT 16 17 33
CONECT 17 18 19 34
CONECT 18 35 36 37
CONECT 19 38 39 40
SPDBVT 1.0000000000 0.0000000000 0.0000000000
SPDBVT 0.0000000000 1.0000000000 0.0000000000
SPDBVT 0.0000000000 0.0000000000 1.0000000000
SPDBVT 0.0000000000 0.0000000000 0.0000000000
SPDBVT 0.0000000000 0.0000000000 0.0000000000
SPDBVV default;
SPDBVV 45.752312478050 1769.439927720726 20.000000000000
SPDBVV 0.8492806468 0.0177824961 0.5276420811
SPDBVV 0.4171748744 0.5899083148 -0.6913561342
SPDBVV -0.3235544887 0.8072744038 0.4935793046
SPDBVV 46.9440002441 44.7815017700 17.6585006714
SPDBVV 0.0000000000 0.0000000000 0.0000000000
SPDBVf 23
SPDBVl 1.00 1.00 1.00
SPDBVb 0.00 0.00 0.00
END
I have also tried the same file without numbers in atom names and
without connections.
Any help will be hightly appreciated.
Sincerely yours,
V. Tanchuk
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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