[gmx-users] add a group to an amino acid
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 9 10:42:15 CET 2010
On 9/11/2010 8:19 PM, hengame fallah wrote:
> Thanks Justin,
> actually the protein that i want to simulate consists of two amino
> acids: PHE and BOC
> BOC is an unusual amino acid as you know.
> It has a Cl instead of HZ in PHE and has one extra CH2 in comparison
> to PHE
So that probably means you'll have to pay care to the [bonds] section in
the .rtp file. The only bonds GROMACS knows about are the ones in the
.rtp. They have to be right. The errors below look like you haven't done
it right.
> I finally defined a residue BOC in opls .rtp file:
>
> [ BOC ]
> [ atoms ]
> N opls_238 -0.500 1
> H opls_241 0.300 1
> CA opls_224B -0.005 1
> HA1 opls_140 0.060 1
> HA2 opls_140 0.060 1
> CB opls_149 0.140 2
> HB1 opls_140 0.060 2
> CG1 opls_145 -0.115 2
> CD1 opls_145 -0.115 3
> HD1 opls_146 0.115 3
> CD2 opls_145 -0.115 4
> HD2 opls_146 0.115 4
> CE1 opls_145 -0.115 5
> HE1 opls_146 0.115 5
> CE2 opls_145 -0.115 6
> HE2 opls_146 0.115 6
> CZ opls_145 0.885 7
> Cl opls_264 -1.000 7
> CG2 opls_071 -0.005 8
> HG1 opls_140 0.060 8
> HG2 opls_140 0.060 8
> C opls_235 0.700 9
> O opls_236 -0.700 9
>
> the ending part of my PDB is:
> ...
> ATOM 38 HE2 PHE 2 -6.946 8.455 4.409
> ATOM 39 CZ PHE 2 -5.456 10.015 4.624
> ATOM 40 HZ PHE 2 -5.887 10.646 3.828
> ATOM 41 N BOC 3 -1.862 5.210 5.333
> ATOM 42 H BOC 3 -2.325 4.344 5.618
> ATOM 43 CA BOC 3 -1.001 5.232 4.169
> ATOM 44 HA1 BOC 3 -0.540 6.235 4.026
HA2 is missing here, per your .rtp
> ATOM 45 CB BOC 3 -1.797 4.794 2.924
> ATOM 46 HB1 BOC 3 -2.244 3.809 3.204
> ATOM 47 CG1 BOC 3 -2.976 5.730 2.589
> ATOM 48 CG2 BOC 3 -0.935 4.544 1.698
> ATOM 49 CD1 BOC 3 -1.231 3.466 0.845
> ATOM 50 HD1 BOC 3 -2.070 2.790 1.081
> ATOM 51 CD2 BOC 3 0.120 5.408 1.353
> ATOM 52 HD2 BOC 3 0.357 6.277 1.986
> ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312
> ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964
> ATOM 55 CE2 BOC 3 0.881 5.182 0.197
> ATOM 56 HE2 BOC 3 1.706 5.870 -0.054
> ATOM 57 CZ BOC 3 0.591 4.093 -0.639
> ATOM 58 C BOC 3 -2.565 7.148 2.291
> ATOM 59 O BOC 3 -2.716 8.035 3.131
> ATOM 60 CL BOC 3 1.525 3.816 -2.062
> ATOM 61 HA2 BOC 3 -0.172 4.511 4.360
> ATOM 62 HG1 BOC 3 -3.530 5.331 1.707
> ATOM 63 HG2 BOC 3 -3.708 5.729 3.431
>
> Now i got t this error:
> ...
> There are 1 chains and 0 blocks of water and 3 residues with 63 atoms
>
> chain #res #atoms
> 1 ' ' 3 63
>
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening library file /usr/share/gromacs/top/ffoplsaa.atp
> Atomtype 1
> Reading residue database... (ffoplsaa)
> Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
> Residue 57
> Sorting it all out...
> Opening library file /usr/share/gromacs/top/ffoplsaa.hdb
> Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb
> Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.69#
> Processing chain 1 (63 atoms, 3 residues)
> There are 3 donors and 3 acceptors
> There are 4 hydrogen bonds
> Checking for duplicate atoms....
> Opening library file /usr/share/gromacs/top/specbond.dat
> 7 out of 7 lines of specbond.dat converted succesfully
> N-terminus: NH3+
> C-terminus: COO-
> Now there are 3 residues with 68 atoms
> Making bonds...
> Warning: Long Bond (52-53 = 0.334847 nm)
> Warning: Long Bond (52-55 = 0.334912 nm)
> Warning: Long Bond (63-64 = 0.271173 nm)
> Warning: Long Bond (63-65 = 0.347808 nm)
> Warning: Long Bond (63-66 = 0.31288 nm)
This is telling you the connectivity in your .rtp doesn't match the
spatial arrangement very well. Go back and check the .rtp file.
> Opening library file /usr/share/gromacs/top/aminoacids.dat
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.7
> Source code file: ../../../../src/kernel/add_par.c, line: 233
>
> Fatal error:
> Atom HB11 not found in rtp database in residue BOC, it looks a bit
> like HB1
pdb2gmx is probably hopelessly confused by now. Fix the other issues and
try again.
Mark
> -------------------------------------------------------
> ...
>
> What should i do?
>
>
> On Sun, Nov 7, 2010 at 4:49 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> hengame fallah wrote:
>
> Hi,
> I'm using the OPLS force field.
>
> [ PHE ]
> [ atoms ]
> N opls_238 -0.500 1
> H opls_241 0.300 1
> CA opls_224B 0.140 1
> HA opls_140 0.060 1
> CB opls_149 -0.005 2
> HB1 opls_140 0.060 2
> HB2 opls_140 0.060 2
> CG opls_145 -0.115 2
> CD1 opls_145 -0.115 3
> HD1 opls_146 0.115 3
> CD2 opls_145 -0.115 4
> HD2 opls_146 0.115 4
> CE1 opls_145 -0.115 5
> HE1 opls_146 0.115 5
> CE2 opls_145 -0.115 6
> HE2 opls_146 0.115 6
> CZ opls_145 -0.115 7
> HZ opls_146 0.115 7
> C opls_235 0.500 8
> O opls_236 -0.500 8
>
> I want to attach "CL" atom instead of HZ
> i made my pdb but when i use pdb2gmx, it adds HZ automatically
> in gro and top files.
> What should i do to get rid of this HZ and attach CL instead.
>
>
> If the .rtp entry says to build PHE with those constituent atoms,
> it will do so. You can make a custom .rtp entry that has CL
> instead of HZ.
>
>
> (I edited top and gro files and remove HZ from them, it seemed
> to work properly at first, but when i tried to do energy
> minimization, it had errors in top file
> and i realized that it couldn't recognized the bond between
> CL and CZ):
>
> ERROR 1 [file topol.top, line 150]:
> No default Bond types
>
>
> ERROR 2 [file topol.top, line 422]:
> No default Angle types
>
>
> ERROR 3 [file topol.top, line 423]:
> No default Angle types
>
>
> All of these errors indicate that OPLS cannot accommodate such a
> species. Making ad hoc changes to the topology often does this.
> Look at what these lines contain and you will be able to identify
> the relevant parameters that are missing.
>
> <snip>
>
>
> 66 opls_401 5 CL CL 26 -1
> 35.453 ; qtot -1.06
>
>
> I would seriously question the validity of doing this. Is it
> really correct to put (essentially) a Cl- ion on a Phe ring and
> call it correct? Proper parameterization is a very challenging
> task, and I doubt what you've proposed here is valid.
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> -Justin
>
>
> ...
> [ bonds ]
> ...
> 59 66 1
> 60 61 1
> 60 62 1
> 63 64 1
> 63 65 1
> ...
> [ angles ]
> ...
> 58 57 59 1
> 55 59 57 1
> 55 59 66 1
> 57 59 66 1
> 45 60 61 1
> 45 60 62 1
> 61 60 62 1
> 64 63 65 1
> ...
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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