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

[Justin Lemkul]

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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