[gmx-users] aminoacids.n.tdb
Emine Deniz Tekin
edeniztekin at gmail.com
Tue Apr 12 14:30:29 CEST 2011
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.
*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 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 ]
[ 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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