[gmx-users] add parameter

[Malihe Hasanzadeh]

Dear Justin,
Thank you for your reply. I have parameters from some manuscript and add
all of them in force field. There is two parts of dihedral types in
ffbonded.itp that one of them has func=4 and another has func=9. Also I
have two types of parameters for dihedral;* Proper* and* Improper *dihedral
that the proper types have* scale=1, 2 or 3 *and* periodicity=**1, 2
or 3. *Since
some of *Proper types* are the same with different Phase, V and Periodicity
number, so I think, I should add all of them ( proper and improper
parameters) in second part with func=9 and ignore scale number for *Proper
types*. Because when I add them in first part with func=4 gave error. I see
manual but I couldn't find where do I add them.

for example:

*Proper types*
dihedral types       scaling          phase
V(kj/mol)                    periodicity

O   C   OQ  HQ         1                   0.0                  7.9496
                     1  ;
O   C   OQ  HQ         1                180.0                  9.6232
                    2  ;

*Improper types*
dihedral types                 phase
V(kj/mol)                    periodicity

CA   CA   C  HQ             180.0                  9.6232
        2  ;

Could you please help me , where do I add the parameters of proper and
improper types in forcefield and what is the func number for them?
Thanks
Malihe







On Fri, Feb 12, 2016 at 5:12 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/11/16 12:03 PM, Malihe Hasanzadeh wrote:
>
>> Hi
>> I have three water molecules and one new residue that I want to add their
>> parameters to force field Amber99sb. One of water molecules has only one
>> hydrogen, and since I want to prevent from replacing with SOL in solvation
>> step, So I define them as new residue in .rtp file:
>>
>> [ INN ]
>>   [ atoms ]
>>     H1    H           0.384620     1
>>      O    O          -0.671930     2
>>     H2    H           0.384620     3
>>
>>
>> [ INT ]
>>   [ atoms ]
>>     H1    H           0.286310     1
>>      O    O          -0.341910     2
>>     H2    H           0.286310     3
>>
>>
>> [ INB ]
>>   [ atoms ]
>>     H1    H           0.477860     1
>>      O    O          -1.092580     2
>> Also define them in .dat file as Protein  and in .hdb file as below:
>>
>>
> Defining these residues as protein is not necessary.
>
> INN    2
>> 1    7    H1    O
>> 1    7    H2    O
>> INT    2
>> 1    7    H1    O
>> 1    7    H2    O
>> INB    1
>> 1    7    H1    O
>>
>> But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em,
>> gives segmentation fault! when I remove their parameters in .hdb file, it
>> is done but without any hydrogen for them, just three oxygen atoms in
>> em.gro!
>>
>>
> This is because you would have had to invoke -missing with pdb2gmx and
> yield something totally useless.
>
> Immediate seg faults are indicative of complete instability.  Note that
> none of your .rtp entries have [bonds] defined, so you probably just have
> particles very close to one another (e.g. as they would be in a real
> molecule) but no covalent attachment, so they likely just fly apart.
>
> Also I have another problem with that new residue, this residue is like a
>> Lys but has two carbonyl groups binded to extra carbon instead of amino
>> group in Lys. So I used Lys parameters for that and add some bonds and
>> atoms to it:
>>
>> [ NEW ] ;
>>   [ atoms ]
>>      N       N
>>      H       H
>>     CA       CT
>>     HA        H1
>>     CB       CT
>>    HB1       HC
>>    HB2       HC
>>     CG      CT
>>    HG1      H
>>    HG2      H
>>     CD      CT
>>    HD1      HC
>>    HD2      HC
>>     CE      CT
>>    HE1      HP
>>    HE2      HP
>>     NZ      N
>>     HZ      H
>>     CX      C
>>    OQ1     O
>>    OQ2     O
>>      C      C
>>      O      O
>>   [ bonds ]
>>       N     H
>>       N    CA
>>      CA    HA
>>      CA    CB
>>      CA     C
>>      CB   HB1
>>      CB   HB2
>>      CB    CG
>>      CG   HG1
>>      CG   HG2
>>      CG    CD
>>      CD   HD1
>>      CD   HD2
>>      CD    CE
>>      CE   HE1
>>      CE   HE2
>>      CE    NZ
>>      NZ    HZ
>>      NZ    CX
>>       C     O
>>      CX   OQ1
>>      CX   OQ2
>>   [ impropers ]
>>      -C    CA     N     H
>>      CA    +N     C     O
>> when I added only atoms parameters in .rtp file, finally in em.gro file
>> there wasn't any bond between atoms of new residue and when I added bond
>>
>
> As you should expect.  See above.  [bonds] is a mandatory directive (which
> is also stated clearly in the manual).
>
> parameters also, in grompp gives 10 error about "default angel and
>> dihedral"! I find the number of angels in .top file and added them to
>> ffbonded.itp, but anything have no change.
>>
>
> You're adding moieties that don't exist in the force field, unless you
> have parameters from some external source (e.g. something published or
> otherwise available in a force field repository).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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