On 5/7/13 1:04 PM, Sun Moon wrote:
Hi
I have been using the lipids from Prof Tieleman's website and (using Berger
Lipids) in gromacs 4.5.4 I want to try the grompp tool but have encountered
this problem:
Fatal error:
Atomtype C not found
This atomtype belongs to protein functional groups. In lipid.itp, nonbonded
parameters are defined for protein-lipid interactions. If you do not need any
protein-specific terms, delete that section of lipid.itp.
-Justin
Topology file is as the following:
#include "lipid.itp"
#include "dopc.itp"
#include "spc.itp"
#include "ions.itp"
'[ system ]'
; name
DOPC bilayer in water
'[ molecules ]'
; name number
DOPC 128
SOL 4825
lipid.itpis as the following:
[ defaults ]
1 1
[ atomtypes ]
;name mass charge ptype c6 c12
LO 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
LOM 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
LNL 14.0067 0.000 A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
LC 12.0110 0.000 A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
LH1 13.0190 0.000 A 4.03100e-03 1.21400e-05 ;CH1, OPLS
LH2 14.0270 0.000 A 7.00200e-03 2.48300e-05 ;CH2, OPLS
…
DOPC.itpisas the following:
[ moleculetype ]
; Name nrexcl
DOPC 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 LC3 1 DOPC C1 0 0.4000 15.0350
; qtot:0.36
2 LC3 1 DOPC C2 0 0.4000 15.0350
; qtot:0.72
3 LC3 1 DOPC C3 0 0.4000 15.0350
; qtot:1.08
4 LNL 1 DOPC N4 0 -0.5000 14.0067 ;
qtot:0.76
5 LH2 1 DOPC C5 0 0.3000 14.0270
; qtot:1.0
6 LC2 1 DOPC C6 1 0.4000 14.0270
; qtot:1.0
..
DOPC.grofile as the following:
128 DOPC in water
21387
1DOPC C1 1 4.048 0.461 2.197 -0.4628 -0.6241 -0.6552
1DOPC C2 2 4.064 0.596 2.395 -0.1879 0.0104 -0.0154
1DOPC C3 3 4.110 0.366 2.405 -0.5498 -0.8024 -0.0627
1DOPC N4 4 4.022 0.466 2.341 0.5789 -0.0490 -0.4766
1DOPC C5 5 3.877 0.457 2.361 0.5625 0.0560 -0.5460
1DOPC C6 6 3.823 0.315 2.343 0.0671 0.1818 -0.0962
…..
Many thanks for your help in advance!
Sun
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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