[gmx-users] aminoacids.n.tdb
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Apr 19 02:20:00 CEST 2011
On 4/19/2011 6:55 AM, Emine Deniz Tekin wrote:
> 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.)
Looks about right.
> Just to be sure, could you have a look at the file (I used gb_10
> between C and +N instead of gb_19).
I don't know anything about those atom types or force field. Use your
own judgment.
Mark
> [ DPP ]
>
> [ atoms ]
>
> CALP20.000000
>
> CBLP20.000001
>
> CGLP20.000002
>
> CDLP20.000003
>
> CELP30.000004
>
> CLC0.4505
>
> OLO-0.4505
>
> [ bonds ]
>
> CACB1 0.15300E+00 0.33470E+06
>
> CCA1 0.15300E+00 0.33470E+06
>
> CBCG1 0.15300E+00 0.33470E+06
>
> CGCD1 0.15300E+00 0.33470E+06
>
> CDCE1 0.15300E+00 0.33470E+06
>
> CO1 0.12300E+00 0.50210E+06
>
> C+Ngb_10
>
> [ angles ]
>
> CCACB1 0.11100E+03 0.46020E+03
>
> CACBCG1 0.11100E+03 0.46020E+03
>
> CBCGCD1 0.11100E+03 0.46020E+03
>
> CGCDCE1 0.11100E+03 0.46020E+03
>
> OCCA1 0.12100E+03 0.50210E+03
>
> CAC+Nga_19
>
> OC+Nga_33
>
> [ dihedrals ]
>
> CCACBCG10.05.863
>
> CACBCGCD3
>
> CBCGCDCE3
>
> [ impropers ]
>
> CCA+NOgi_1
>
> Best regards,
>
> Deniz
>
> On Tue, Apr 12, 2011 at 4:26 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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 concatenatedthe 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 ]
>>
>> C34LC0.80018
>>
>> O35LO-0.6018
>>
>> C36LP2019
>>
>> C37LP2020
>>
>> C38LP2021
>>
>> C39LP2022
>>
>> C40LP20 23
>>
>> C41LP2024
>>
>> C42LP2025
>>
>> C43LP2026
>>
>> C44LP2027
>>
>> C45LP2028
>>
>> C46LP3029
>>
>> [ bonds ]
>>
>> ;aiaj funct
>>
>> 34351 0.12300E+00 0.50210E+06
>>
>> 34361 0.15300E+00 0.33470E+06
>>
>> 36371 0.15300E+00 0.33470E+06
>>
>> 37381 0.15300E+00 0.33470E+06
>>
>> 38391 0.15300E+00 0.33470E+06
>>
>> 39401 0.15300E+00 0.33470E+06
>>
>> 40411 0.15300E+00 0.33470E+06
>>
>> 41421 0.15300E+00 0.33470E+06
>>
>> 42431 0.15300E+00 0.33470E+06
>>
>> 43441 0.15300E+00 0.33470E+06
>>
>> 44451 0.15300E+00 0.33470E+06
>>
>> 45461 0.15300E+00 0.33470E+06
>>
>> [ angles ]
>>
>> ;aiajak funct
>>
>> 3436371 0.11100E+03 0.46020E+03
>>
>> 3534361 0.12100E+03 0.50210E+03
>>
>> 3637381 0.11100E+03 0.46020E+03
>>
>> 3738391 0.11100E+03 0.46020E+03
>>
>> 3839401 0.11100E+03 0.46020E+03
>>
>> 3940411 0.11100E+03 0.46020E+03
>>
>> 4041421 0.11100E+03 0.46020E+03
>>
>> 4142431 0.11100E+03 0.46020E+03
>>
>> 4243441 0.11100E+03 0.46020E+03
>>
>> 4344451 0.11100E+03 0.46020E+03
>>
>> 4445461 0.11100E+03 0.46020E+03
>>
>> [ dihedrals ]
>>
>> ;aiajakal functphi0cpmult
>>
>> 3436373810.05.863
>>
>> 363738393
>>
>> 373839403
>>
>> 383940413
>>
>> 394041423
>>
>> 404142433
>>
>> 414243443
>>
>> 424344453
>>
>> 434445463
>>
>>
>> Best regards,
>>
>> Deniz
>>
>>
>>
>>
>>
>> On Sun, Apr 10, 2011 at 3:02 AM, Mark Abraham
>> <Mark.Abraham at anu.edu.au <mailto: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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>
>
> --
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