[gmx-users] add parameter
Justin Lemkul
jalemkul at vt.edu
Sat Feb 13 06:10:22 CET 2016
On 2/12/16 11:06 AM, Malihe Hasanzadeh wrote:
> 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.
>
Table 5.5 has all the information you need. Function type 4 is a periodic
improper dihedral, type 9 is a proper dihedral that allows multiple terms.
-Justin
> 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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--
==================================================
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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