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

lammps lammps lammp2forum at gmail.com
Sun Oct 10 03:34:34 CEST 2010


get it

Thanks very much!!



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

>
>
> lammps lammps wrote:
>
>> 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?)
>>
>
> It should pertain to the number of bonds you want that atom to form, aside
> from those in the .rtp entry.  See the line for HIS NE2, which forms one
> bond to FE, but certainly forms other bonds to atoms in the HIS residue.
>
>
>  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
>> ą10% ( It seems the unreasonable length can result in the unexpected bond.
>> does it? )
>>
>
> I don't understand your question.  If you define a bond at, i.e. 0.1 nm,
> pdb2gmx will build a bond if the distance between the two atoms is 0.9 - 1.1
> nm.  An unreasonable bond will only be formed if you provide an unreasonable
> search distance.
>
>
>  8.the new name for residue A ( Why new residue name?)
>>
>
> This isn't always relevant.  Note that most of the entries in specbond.dat
> remain unchanged.  The only instances of the residue name changing are
> related to force field-specific disulfide conventions (i.e., CYS vs. CYS2).
>
> -Justin
>
>  9.the new name for residue B
>>  Thanks again.
>>  2010/10/9 Justin A. Lemkul <jalemkul at vt.edu <mailto: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> <mailto: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>
>>           <mailto: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>
>>           <mailto: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
>>           --
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>>
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>>
>>
>>        --         wende
>>
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
>>
>>
>> --
>> 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
>
> ========================================
> --
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-- 
wende
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