[gmx-users] how to write a rtp file for amido amine
lammp2forum at gmail.com
Sat Oct 9 16:42:06 CEST 2010
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
8.the new name for residue A ( Why new residue name?)
9.the new name for residue B
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
> 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.
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> 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
> gmx-users mailing list gmx-users at gromacs.org
> 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
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