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" <jalem...@vt.edu>
Sent: Wednesday, August 12, 2009 9:23 PM
To: "Discussion list for GROMACS users" <gmx-users@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:nicegrom...@live.cl>
*Sent:* Wednesday, August 12, 2009 8:28 PM
*To:* gmx-users@gromacs.org <mailto:gmx-users@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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
