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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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