[gmx-users] aminoacids.n.tdb
Emine Deniz Tekin
edeniztekin at gmail.com
Mon Apr 18 22:55:44 CEST 2011
Hi Mark,
Thanks again. Your suggestion of introducing the lauroic acid as a
pseudo-amino acid seems to solve my problem. Below is my corrected
"aminoacids.rtp" file for the 6-Carbon case as a test. (I used the Berger
lipid parameters.) Just to be sure, could you have a look at the file (I
used gb_10 between C and +N instead of gb_19).
[ DPP ]
[ atoms ]
CA LP2 0.00000 0
CB LP2 0.00000 1
CG LP2 0.00000 2
CD LP2 0.00000 3
CE LP3 0.00000 4
C LC 0.450 5
O LO -0.450 5
[ bonds ]
CA CB 1 0.15300E+00 0.33470E+06
C CA 1 0.15300E+00 0.33470E+06
CB CG 1 0.15300E+00 0.33470E+06
CG CD 1 0.15300E+00 0.33470E+06
CD CE 1 0.15300E+00 0.33470E+06
C O 1 0.12300E+00 0.50210E+06
C +N gb_10
[ angles ]
C CA CB 1 0.11100E+03 0.46020E+03
CA CB CG 1 0.11100E+03 0.46020E+03
CB CG CD 1 0.11100E+03 0.46020E+03
CG CD CE 1 0.11100E+03 0.46020E+03
O C CA 1 0.12100E+03 0.50210E+03
CA C +N ga_19
O C +N ga_33
[ dihedrals ]
C CA CB CG 1 0.0 5.86 3
CA CB CG CD 3
CB CG CD CE 3
[ impropers ]
C CA +N O gi_1
Best regards,
Deniz
On Tue, Apr 12, 2011 at 4:26 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote:
>
>
> Hi Mark,
>
>
> Thank you for your reply. But, I couldn’t understand very well what you
> meant “you can make one that uses backbone-style linking. Most of the
> forcefields will have examples of non-amino-acid terminating residues -
> these make a single peptide bond just like yours does.”. So, let me
> explain the problem a little more. I would be happy if you could expound
> upon your reply.
>
>
> *1)* I prepared the *rtp *entry for the lauroic acid (see below) and
> add the lipid parameters to the relevant sections of the *ffnonbonded.itp*and
> *ffbonded.itp* files.
>
>
> That is not an .rtp entry, see below. Look at some .rtp entries and see how
> they make backbone bonds. That is what I understand you want to do - make a
> peptide bond as if lauroic acid was an amino acid.
>
>
> *2)* I added the lauroic acid as a "Non-Protein” in the *
> residuetypes.dat *file and also I introduced the atom types (LO: 15.9994,
> LC: 12.0110, LP2: 14.0270, LP3: 15.0350) in the *atomtypes.atp.*
>
> *3) *I concatenated the structure files of a 8-residue-peptide* *and
> lauroic acid as *system.gro. *Then, using “pdb2gmx -ter”, I obtained the *topol.top,
> conf.gro* and *posre.itp* for *the whole system.* (I chose : start
> terminus VAL-2: NH2 and end terminus ASP-9: COO-)
>
> *4)* But when I looked into *conf.gro* with the VMD, I see that the
> peptide bond is formed between the
>
>
> No bond shown by VMD is relevant. It's guessing based on the coordinates in
> your .gro file. Your bonded atoms are in your .top file. VMD knows nothing
> about your .top file.
>
>
> lauroic acid (C34) and the N terminal of the Valine. However, second H of
> the N is still there and it is making another bond with C34 of lauroic acid.
> The strange thing is: C34 is double bonded to O35, Carbon makes four
> bonds.
>
> How can I get rid of that H?
>
> [ DPP ]
>
>
> This is not an .rtp entry. The [bonds] section must refer to atom names. I
> can only suppose pdb2gmx is warning about or ignoring everything after your
> [atoms] section.
>
> Look in the .rtp and chapter 5 of the manual how terminating
> pseudo-residues like ACE work. Do something analogous for lauroic acid.
>
> Mark
>
>
> [ atoms ]
>
> C34 LC 0.800 18
>
> O35 LO -0.60 18
>
> C36 LP2 0 19
>
> C37 LP2 0 20
>
> C38 LP2 0 21
>
> C39 LP2 0 22
>
> C40 LP2 0 23
>
> C41 LP2 0 24
>
> C42 LP2 0 25
>
> C43 LP2 0 26
>
> C44 LP2 0 27
>
> C45 LP2 0 28
>
> C46 LP3 0 29
>
> [ bonds ]
>
> ; ai aj funct
>
> 34 35 1 0.12300E+00 0.50210E+06
>
> 34 36 1 0.15300E+00 0.33470E+06
>
> 36 37 1 0.15300E+00 0.33470E+06
>
> 37 38 1 0.15300E+00 0.33470E+06
>
> 38 39 1 0.15300E+00 0.33470E+06
>
> 39 40 1 0.15300E+00 0.33470E+06
>
> 40 41 1 0.15300E+00 0.33470E+06
>
> 41 42 1 0.15300E+00 0.33470E+06
>
> 42 43 1 0.15300E+00 0.33470E+06
>
> 43 44 1 0.15300E+00 0.33470E+06
>
> 44 45 1 0.15300E+00 0.33470E+06
>
> 45 46 1 0.15300E+00 0.33470E+06
>
> [ angles ]
>
> ; ai aj ak funct
>
> 34 36 37 1 0.11100E+03 0.46020E+03
>
> 35 34 36 1 0.12100E+03 0.50210E+03
>
> 36 37 38 1 0.11100E+03 0.46020E+03
>
> 37 38 39 1 0.11100E+03 0.46020E+03
>
> 38 39 40 1 0.11100E+03 0.46020E+03
>
> 39 40 41 1 0.11100E+03 0.46020E+03
>
> 40 41 42 1 0.11100E+03 0.46020E+03
>
> 41 42 43 1 0.11100E+03 0.46020E+03
>
> 42 43 44 1 0.11100E+03 0.46020E+03
>
> 43 44 45 1 0.11100E+03 0.46020E+03
>
> 44 45 46 1 0.11100E+03 0.46020E+03
>
> [ dihedrals ]
>
> ; ai aj ak al funct phi0 cp mult
>
> 34 36 37 38 1 0.0 5.86 3
>
> 36 37 38 39 3
>
> 37 38 39 40 3
>
> 38 39 40 41 3
>
> 39 40 41 42 3
>
> 40 41 42 43 3
>
> 41 42 43 44 3
>
> 42 43 44 45 3
>
> 43 44 45 46 3
>
>
> Best regards,
>
> Deniz
>
>
>
>
> On Sun, Apr 10, 2011 at 3:02 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>> On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote:
>>
>>>
>>> Hi Gromacs users,
>>>
>>> I want to covalently link the lauroic acid to the Valine residue (it is a
>>> peptide (amide) bond), I know that I should update the specbond.dat.But
>>> before updating this file, I need the NH as an N terminal of the first
>>> residue (Valine).When I used pdb2gmx with the –ter flag, I got either NH3,
>>> NH2 or None instead of NH.So, I add the [NH] directive in the
>>> aminoacids.n.rtp file, as follows;
>>>
>>>
>>> [ NH ]
>>>
>>> [ replace ]
>>>
>>> ; old-namenew-typenew-massnew-charge
>>>
>>> NLN14.0067-0.31
>>>
>>> CACH113.0190.127
>>>
>>> [ add ]
>>>
>>> 12HNCAC
>>>
>>> ;atom_typemasscharge
>>>
>>> H1.0080.31
>>>
>>> [ delete ]
>>>
>>> H
>>>
>>> [ bonds ]
>>>
>>> NHgb_2
>>>
>>> [ angles ]
>>>
>>> CANHga_11
>>>
>>> [ dihedrals ]
>>>
>>> HNCACgd_29
>>>
>>>
>>>
>>> (ps. I wrote the charges of N, CA and H according to values defined in
>>> topol.top and also I used the Gromos96 53a6 force field)
>>>
>>>
>>> Then, I used the pdb2gmx with –ter, I could see:
>>>
>>> Select start terminus type for VAL
>>>
>>> 0: NH
>>>
>>> 1: NH3+
>>>
>>> 2: NH2
>>>
>>> 3: None
>>>
>>>
>>> Finally, I got thetopol.top, posre itp and conf.gro files. But when I
>>> looked into conf.gro, I see that I am getting “None”. How can I get the NH ?
>>>
>>>
>> Coordinating multiple "moving parts" like the specbond and terminus-fixing
>> is probably a recipe for trouble.
>>
>> Since you have to make an .rtp entry for lauroic acid anyway, you can make
>> one that uses backbone-style linking. Most of the forcefields will have
>> examples of non-amino-acid terminating residues - these make a single
>> peptide bond just like yours does. Now you can ignore the specbond and
>> terminus-fixing mechanisms entirely.
>>
>> Mark
>> --
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>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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