On 5/11/13 5:37 AM, Sun Moon wrote:
Hi,
I am doing pure membrane simulation in DOPC environment (using Berger
Lipids) in Gromacs 4.0.7 I want to try the grompp tool but have
encountered this problem:
Fatal error:
Atomtype OW not found
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
……………….
Inlipid.itp file, lipid-SPC/SPCE interactions is defined:
;;
lipid-SPC/SPCE interactions
LO OW 1 2.50200e-03 2.06700e-06
LOM OW 1 2.50200e-03 2.06700e-06
LNL OW 1 2.98000e-03 3.25900e-06
LC OW 1 3.59800e-03 6.04400e-06
LH1 OW 1 3.26800e-03 5.71200e-06
LH2 OW 1 4.30700e-03 8.17000e-06
LP OW 1 4.92600e-03 8.21000e-06
LOS OW 1 2.60500e-03 2.24100e-06
…….
Spc.itpfile from gromos
FF as the following:
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 SOL OW 1 -0.82
2 HW 1 SOL HW1 1 0.41
3 HW 1 SOL HW2 1 0.41
…
…………………….
dopc.groas the following:
….
129SOL OW 6913 4.231 0.169 1.664 -0.1323 -0.0792 0.5040
129SOL HW1 6914 4.146 0.202 1.704 -0.3042 0.1272 -0.0232
129SOL HW2 6915 4.263 0.089 1.715 -0.7744 -0.3135 0.5523
130SOL OW 6916 4.513 4.020 6.355 0.3593 -0.2561 0.3581
130SOL HW1 6917 4.591 3.980 6.403 -0.2604 -0.1715 1.4756
130SOL HW2 6918 4.545 4.090 6.291 1.1718 0.0930 1.1277
……..
What should I do?
You need to introduce OW (and probably HW) as valid atom types within the force
field. The lipid.itp file was created to be used in conjunction with a Gromos
parameter set (originally Gromos87, but can also be used with Gromos96) that
takes care of protein and water atom types.
-Justin
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
