Moeed wrote:
Hello,
I am trying to generate gro and top file with pdb2gmx program. I have
made a copy of ffoplsaa.rtp from library to working directory and added
Hexane molecule residue to the beginning of the ffoplsaa.rtp.
*****************************************.
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; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove propers over the same bond as an improper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1 1 3 1 0
[ HEX ]
[ atoms ]
C1 opls_157 -0.180 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
H13 opls_140 0.060 1
C2 opls_158 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_158 0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_158 -0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
C5 opls_158 -0.120 5
H51 opls_140 0.060 5
H52 opls_140 0.060 5
C6 opls_157 -0.180 6
H61 opls_140 0.060 6
H62 opls_140 0.060 6
H63 opls_140 0.060 6
[ bonds ]
C1 H11
C1 H12
C1 H13
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 C5
C5 H51
Here's a problem (although not one that should cause pdb2gmx to somehow fail).
You haven't defined any bonds to C5-C6 or C6 to any of its hydrogens.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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