Re: [gmx-users] how to write a rtp file for amido amine
get it Thanks very much!! 2010/10/10 Justin A. Lemkul > > > lammps lammps wrote: > >> Thanks for Mark and Justin's help. But I have new questions as follows: >> CYS SG 1 HEMEFE 2 0.25CYS2HEME >> 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 mailto:jalem...@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 ><mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au >> >><mailto:mark.abra...@anu.edu.au>>> >> >> >> >> >> - Original Message - >> From: lammps lammps ><mailto:lammp2fo...@gmail.com> >> <mailto:lammp2fo...@gmail.com <mailto:lammp2fo...@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 ><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@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 ] >>>C1opls_245-0.0501 > . >>> [ bonds ] >>>C1-N7 >>> ... >>>C6N7 >> > 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 listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> &g
Re: [gmx-users] how to write a rtp file for amido amine
lammps lammps wrote:
Thanks for Mark and Justin's help. But I have new questions as follows:
CYS SG 1 HEMEFE 2 0.25CYS2HEME
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
±10% ( 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 mailto:jalem...@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 mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>
- Original Message -
From: lammps lammps mailto:lammp2fo...@gmail.com>
<mailto:lammp2fo...@gmail.com <mailto:lammp2fo...@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 mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@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 ]
>C1opls_245-0.0501 > .
> [ bonds ]
>C1-N7
> ...
>C6N7
> 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 listgmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
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<mailto:gmx-users-requ...@gromacs.org>
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<mailto:gmx-users-requ...@gromacs.org>>.
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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
===
Re: [gmx-users] how to write a rtp file for amido amine
Thanks for Mark and Justin's help. But I have new questions as follows: CYS SG 1 HEMEFE 2 0.25CYS2HEME 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 > > > 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.abra...@anu.edu.au>> >> >> >> >> >>----- Original Message ----- >> From: lammps lammps ><mailto:lammp2fo...@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 > <mailto:gmx-users@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 ] >> >C1opls_245-0.0501 > . >> > [ bonds ] >> >C1-N7 >> > ... >> >C6N7 >>> 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 listgmx-users@gromacs.org >><mailto:gmx-users@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-requ...@gromacs.org >><mailto:gmx-users-requ...@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 listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- wende -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to write a rtp file for amido amine
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 <mailto:mark.abra...@anu.edu.au>>
- Original Message -
From: lammps lammps mailto:lammp2fo...@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 mailto:gmx-users@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 ]
>C1opls_245-0.0501
> .
> [ bonds ]
>C1-N7
> ...
>C6N7
> 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 listgmx-users@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@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 listgmx-users@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
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to write a rtp file for amido amine
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. Thanks in advance. 2010/10/9 Mark Abraham > > > - Original Message - > From: lammps lammps > 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 > > > 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 ] > >C1opls_245-0.0501 > > . > > [ bonds ] > >C1-N7 > > ... > >C6N7 > >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 listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- wende -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to write a rtp file for amido amine
- Original Message - From: lammps lammps 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 > 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 ] >C1opls_245-0.0501 > . > [ bonds ] > C1-N7 > ... >C6N7 >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 listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to write a rtp file for amido amine
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 ] C1opls_245-0.0501 . [ bonds ] C1-N7 ... C6N7 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. Thanks in advance. -- wende <>-- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
