[gmx-users] Making itp files
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 8 01:00:25 CEST 2009
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
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list