[gmx-users] how to write a rtp file for amido amine

[lammps lammps]

Thanks for Mark and Justin's help. But I have new questions as follows:


CYS     SG      1       HEME    FE      2       0.25    CYS2    HEME

1.residue name A
2.atom name A
3.number of bonds that this atom can form (does the number include
the bonds of atom with H atoms?)
4.residue name B
5.atom name B
6.number of bonds that this atom can form
7.the reference length for searching for candidate bonds, the margin
is ±10%( It seems the unreasonable length can result in the unexpected
bond. does
it? )
8.the new name for residue A ( Why new residue name?)
9.the new name for residue B

Thanks again.


2010/10/9 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> lammps lammps wrote:
>
>> Hi  Mark,
>>
>> Thanks for your reply. But, I do not know the meaning of the columns in
>>  specbonds.dat. I also  do not find any information in the manual 4.0.
>>
>> Could you provide something about the specbonds.dat or give some
>> explanations.
>>
>>
> http://www.gromacs.org/Documentation/File_Formats/specbond.dat
>
> -Justin
>
> Thanks in advance.
>>
>>
>>
>> 2010/10/9 Mark Abraham <mark.abraham at anu.edu.au <mailto:
>> mark.abraham at anu.edu.au>>
>>
>>
>>
>>
>>    ----- Original Message -----
>>    From: lammps lammps <lammp2forum at gmail.com
>>    <mailto:lammp2forum at gmail.com>>
>>    Date: Saturday, October 9, 2010 19:27
>>    Subject: [gmx-users] how to write a rtp file for amido amine
>>    To: Discussion list for GROMACS users <gmx-users at gromacs.org
>>     <mailto:gmx-users at gromacs.org>>
>>
>>     > Hi everybody,
>>     >
>>     > I want to use pdb2gmx command to create a .gro file and a .top
>>    file for PAMAM whose repeat unit is amidoamine ( attached ).
>>     >
>>     >                                                 /
>>     > ---CH2--CH2--CO-NH-CH2-CH2-N    (see the attached figure)
>>     >                                                 \
>>     >
>>     > The atom N have two same branches with --CH2--. I write the rtp
>>    file for it as follows:
>>     >
>>     >  [ atoms ]
>>     >    C1    opls_245    -0.050    1       >  .........
>>     >  [ bonds ]
>>     >    C1    -N7
>>     > .......
>>     >    C6    N7
>>    >     N7    +C1
>>    >     N7    +C1
>>     >
>>     > It seems not work, which gives a wrong top structure. The
>>    question is how can I deal with the two branches of N. Any
>>    suggestion is appreciated.
>>
>>    pdb2gmx is intended only for work with linear heteropolymers. Any
>>    more complex things (e.g. disulfides, branched structures) have to
>>    be engineered using the specbonds.dat mechanism.
>>
>>    Mark
>>    --
>>    gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at
>>    http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>    Please don't post (un)subscribe requests to the list. Use the
>>    www interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>
>>    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> wende
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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 at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
wende
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101009/209c4163/attachment.html>