[gmx-users] add a group to an amino acid

[Justin A. Lemkul]

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
> ...
>  
> 

-- 
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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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