[gmx-users] add a group to an amino acid
hengame fallah
hengame.fallah at gmail.com
Tue Nov 9 10:19:24 CET 2010
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
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
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)
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
-------------------------------------------------------
...
What should i do?
On Sun, Nov 7, 2010 at 4:49 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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