[gmx-users] pdb2gmx : treat CL as C

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> here is all information. I attached  2 attachment to my privious mail. It
> looks 2nd didn't come. Sorry. Here I am giving details.
> 
> I am using opls force field . I added "PCD" as residue name in
> aminoacid.dat file.
> 
> pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter
> 
> i have attached input:dioxin.pdb, output:di.pdb and di.top
> 
> here I have pasted the parameters from .rtp  file.
> 

What is the problem?  It looks like you got everything to work, but the .pdb 
file you've posted is misformatted on the CL lines:

ATOM     14  C14 PCD     1      -2.372  -1.395   0.000  1.00  0.00           C
ATOM     15 CL1  PCD     1       5.070   1.618  -0.001  1.00  0.00          CL

Note how the atom name "CL1" is shifted relative to "C14" so pdb2gmx handled it 
incorrectly.  Formatting is not merely a suggestion!

-Justin

>  [ PCD ]
>  [ atoms ]
>     O  opls_186   -0.3088  1
>    C2  opls_263    0.2336  2
>    C3  opls_263    0.2336  2
>    O4  opls_186   -0.3088  1
>    C5  opls_263    0.2336  2
>    C6  opls_263    0.2336  2
>    C7  opls_263   -0.2325  2
>    C8  opls_263    0.0907  2
>    C9  opls_263    0.0908  2
>   C10  opls_263   -0.2326  2
>   C11  opls_263   -0.2326  2
>   C12  opls_263    0.0907  2
>   C13  opls_263    0.0907  2
>   C14  opls_263   -0.2325  2
>  CL1   opls_264   -0.0986  3
>  CL2   opls_264   -0.0986  3
>  CL3   opls_264   -0.0986  3
>  CL4   opls_264   -0.0986  3
>   H19  opls_146    0.1612  4
>   H20  opls_146    0.1612  4
>   H21  opls_146    0.1612  4
>   H22  opls_146    0.1612  4
> 
> [ bonds ]
>     O  C2
>    C2  C3
>    C3  O4
>    O4  C5
>    C5  C6
>    C6   O
>    C3  C7
>    C7  C8
>    C8  C9
>    C9  C10
>   C10   C2
>   C5   C11
>   C11  C12
>   C12  C13
>   C13  C14
>   C14  C6
>    C8  CL1
>    C9  CL2
>   C12  CL4
>   C13  CL4
>   C10  H19
>    C7  H20
>   C14  H21
>   C11  H22
> 
> 
> 
> 

-- 
========================================

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

========================================