[gmx-users] bad bond in polymer

[nicegromacs]

Hi,
the .rtp

[ POL ]
 [ atoms ]
   CAA  CH3    0.000
   CAB  CH2    0.000
   CAC  CH2    0.000
   CAD  CH2    0.000
   CAE  CH2    0.000
   CAF  CH2    0.000
   CAG  CH1    0.000
   CAH  CH2    0.041
   CAI  CH1    0.107
   CAJ    C    0.352
   OAK   OM   -0.750
   OAL   OM   -0.750
   CAM  CH2    0.044
   CAN    C    0.373
   OAO   OM   -0.709
   OAP   OM   -0.708
[ bonds ]
   CAA  CAB
   CAB  CAC
   CAC  CAD
   CAD  CAE
   CAE  CAF
   CAF  CAG
   CAG  CAH
   CAH  CAI
   CAI  CAJ
   CAI  CAM
   CAJ  OAK
   CAJ  OAL
   CAM  CAN
   CAN  OAO
   CAN  OAP
   CAG -CAM
 [ impropers ]
   CAG  CAF -CAM  CAH
  -CAM -CAN -CAI  CAG
   CAJ  CAI  OAL  OAK
   CAN  CAM  OAP  OAO
   CAI  CAH  CAJ  CAM

--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Wednesday, August 12, 2009 9:23 PM
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer

>
>
> nicegromacs wrote:
>> Hi,
>>  the bad bond appear in the topology (.top) file.
>>
>
> Then it is something you have added.  If you want any useful advice, post 
> the .rtp entries you are using.
>
> -Justin
>
>> veduardo.
>>
>>  Lab. de  Fisicoquímica Molecular
>>  Facultas de Ciencias
>>  Universidad de Chile
>>
>> *From:* nicegromacs <mailto:nicegromacs at live.cl>
>> *Sent:* Wednesday, August 12, 2009 8:28 PM
>> *To:* gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>> *Subject:* [gmx-users] bad bond in polymer
>>
>> Hi gmx-users,
>>
>> I am building a polymer and I've added the monomer unit to the .rtp file. 
>> The final structure appears with an undesired bond between the monomer 
>> units at the extremes of the polymer.
>> How can I prevent the monomers at the end forming the bond?
>>
>> I have read other post like 
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html  but  can 
>> not avoid this problem .
>>
>> Thank you in advance
>>
>> veduardo.
>>
>> Lab. de  Fisicoquímica Molecular
>>
>> Facultas de Ciencias
>>
>> Universidad de Chile
>>
>>  ------------------------------------------------------------------------
>>
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>
> -- 
> ========================================
>
> 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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