[gmx-users] general question about molecule.rtp and pdb2gmx

[Mark Abraham]

.rtp [bonds] requires atom names (because that's all that can be
reliably deduced from the coordinate file input)
.itp/.top [bonds] requires atom numbers (because prior sanity-ization
is assumed) to look up the atom types to look up the interaction
parameters

... and different force fields have slightly different details. Ain't life fun?

Mark

On Tue, Aug 27, 2013 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/27/13 12:30 PM, Valentina wrote:
>>
>> Hi, a general question about writing molecule.rtp and how pdb2gmx treats
>> it.
>>
>> I have a few atom types and a few atoms per each atom type.
>>
>> So a question - when I define interactions, say [ bonds ] can I define
>> them
>> by atomtype, rather that atom number?!
>>
>> *So like this:*
>> [ B31 ]
>>    [ atoms ]
>> ; atomname atomtype charge chargegroup
>>     o1  oc15  -1.00   0
>>     h1  hoz    0.30  0
>>     o2  oc18  -0.875   1
>>     h2  hoy    0.350  1
>>     o3  oc21  -0.875   1
>>     h3  hoy    0.350  1
>>     o4  oc17  -0.875   2
>>     h4  hoy    0.350  2
>>     mg1 mg    1.40    3
>>     al1 ac3    1.35   4
>>     o5  oc16  -0.875   5
>>     h5  hoy    0.350  5
>>     o6  oc20  -0.875   2
>>     h6  hoy    0.350  2
>>     o7  oc19  -0.875   5
>>     h7  hoy    0.350  5
>>     o8  oc15   -1.00    6
>>     h8  hoz    0.30  6
>>     mg2 mg   1.40   7
>>     mg3 mg   1.40   8
>>    [ bonds ]
>>   ; atom1 atom2   parametersindex
>>     oc15 hoz b_oc-h
>>     oc16 hoy b_oc-h
>>     oc17 hoy b_oc-h
>>     oc18 hoy b_oc-h
>>     oc19 hoy b_oc-h
>>     oc20 hoy b_oc-h
>>     oc21 hoy b_oc-h
>>    ac3  oc16    a_oc-ac-h
>>    ac3  oc17    a_oc-ac-h
>>    ac3  oc18    a_oc-ac-h
>>    ac3  oc19    a_oc-ac-h
>>    ac3  oc20    a_oc-ac-h
>>    ac3  oc21    a_oc-ac-h
>>
>> *Rather than like this:*
>> [ B31 ] ;
>>    [ atoms ]
>> ; atomname atomtype charge chargegroup
>>     o1  oc15  -1.00   0
>>     h1  hoz    0.30  0
>>     o2  oc18  -0.875   1
>>     h2  hoy    0.350  1
>>     o3  oc21  -0.875   1
>>     h3  hoy    0.350  1
>>     o4  oc17  -0.875   2
>>     h4  hoy    0.350  2
>>     mg1 mg    1.40    3
>>     al1 ac3    1.35   4
>>     o5  oc16  -0.875   5
>>     h5  hoy    0.350  5
>>     o6  oc20  -0.875   2
>>     h6  hoy    0.350  2
>>     o7  oc19  -0.875   5
>>     h7  hoy    0.350  5
>>     o8  oc15   -1.00    6
>>     h8  hoz    0.30  6
>>     mg2 mg   1.40   7
>>     mg3 mg   1.40   8
>>    [ bonds ]
>>   ; atom1 atom2   parametersindex
>>     o1 h1 b_oc-h
>>     o2 h2 b_oc-h
>>     o3 h3 b_oc-h
>>     o4 h4 b_oc-h
>>     o5 h5 b_oc-h
>>     o6 h6 b_oc-h
>>     o7 h7 b_oc-h
>>     o8 h8 b_oc-h
>>     al1 o5      a_oc-ac-h
>>     al1 o4      a_oc-ac-h
>>     al1 o2      a_oc-ac-h
>>     al1 o7      a_oc-ac-h
>>     al1 o6      a_oc-ac-h
>>     al1 o3      a_oc-ac-h
>>
>
> Defining by type is ambiguous.  An .rtp requires that atom names be used to
> define connectivity.
>
>
>>
>> If I use the 1st I get .top that does not list interactions, just [ atoms
>> ]
>> and #include link to the FF. Is this still OK? Does it read the [ bonds ]
>> interactions or just non bonded?
>>
>
> No, it's not OK.  In that case, you have no bonds at all, so your molecule
> would go flying apart.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
>
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