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