As noted by your rtp entry:
> [ bonds ]
> C1 -C4
> C1 H11
> C1 H12
> C1 C2
> C2 F21
> C2 F22
> C2 +C3
> C3 F31
> C3 F32
> C3 C4
> C4 F4
> C4 Cl4
> C4 +C1
One end of the residue bonds via the C1 to a C4 in the next residue, and the
other end of the residue bonds via the C4 to a C1 in the next residue.
Your beginning and ends to your polymer have to show this, which they currently
do not. The rtp entry for both of them do not say anything about how they bond
to the next residue. It should be more something like this ...
[ Fbg ]
[ bonds ]
C4 +C1
C4 H11
C4 H12
C4 H13
[ Fen ]
[ bonds ]
C1 -C4
C1 H11
C1 H12
C1 H13
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.
> -----Original Message-----
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of cqgzc
> Sent: Tuesday, 19 March 2013 12:50 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
>
> I have successfully construct the polymer chain of length 1 using the
> OPLS
> force field. The rtp file as follow:
>
> ; F2311 - this is an internal residue
> [ Fre ]
> [ atoms ]
> C1 opls_135 -0.568 1
> H11 opls_140 0.274 1
> H12 opls_140 0.273 1
> C2 opls_962 0.373 2
> F21 opls_965 -0.165 2
> F22 opls_965 -0.159 2
> C3 opls_962 0.182 3
> F31 opls_965 -0.133 3
> F32 opls_965 -0.144 3
> C4 opls_963 0.142 4
> F4 opls_965 -0.142 4
> Cl4 opls_151 0.066 4
> [ bonds ]
> C1 -C4
> C1 H11
> C1 H12
> C1 C2
> C2 F21
> C2 F22
> C2 +C3
> C3 F31
> C3 F32
> C3 C4
> C4 F4
> C4 Cl4
> C4 +C1
>
> ; Terminal f2311 residue ("beginning" of chain)
> ; designation arbitrary, C1 is -CH3
> [ Fbg ]
> [ atoms ]
> C1 opls_135 -0.565 1
> H11 opls_140 0.198 1
> H12 opls_140 0.208 1
> H13 opls_140 0.209 1
> [ bonds ]
> C1 H11
> C1 H12
> C1 H13
> ; Terminal f2311 residue ("end" of chain)
> ; designation arbitrary, C1 is -CH3
> [ Fen ]
> [ atoms ]
> C1 opls_135 -0.705 1
> H11 opls_140 0.248 1
> H12 opls_140 0.246 1
> H13 opls_140 0.245 1
> [ bonds ]
> C1 H11
> C1 H12
> C1 H13
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-
> tp5006328p5006428.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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