[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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>>
>>
>>
>> -- 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
>
> ========================================
> --
> 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!
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--
wende
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