On 4/17/13 4:28 AM, Parul tew wrote:
Dear GMX users,
I am working on a protein which I want to simulate in a lipid bilayer
environment (POPC) and want to use OPLS force field for the same. I
followed the chris neale directives to make the necessary changes i.e.
sigma and epsilon, I incorporated the modified atom types of lipids in
oplsaanb_lipid.itp
LO LO 1 15.9994 0 A 0.29599993 0.87869434
;carbonyl O, OPLS"
LOM LOM 1 15.9994 0 A 0.29599993 0.87869434
;carboxyl O, OPLS
I also made changes to the [pair types] and appended them in the
oplsaanb_lipid.itp file
[ pair types ]
; i j func sigma epsilon
LO LO 1 0.29603763 0.10964147
LO LOM 1 0.29603763 0.10964147
LO opls_116 1 0.306316902 0.094663158
and also changed the OW to opls_116 and removed HW lines.
Now I want to generate the tpr file using grompp where I had generated a
topol_popc.top :
--------------------------------------------------------------------------------------------------
; Include chain topologies
#include "oplsaa_lipid.ff/forcefield.itp"
#include "popc.itp"
; Include water topology
#include "oplsaa_lipid.ff/spc.itp"
; System specifications
[ system ]
128-Lipid POPC Bilayer
[ molecules ]
; molecule name nr.
POPC 128
SOL 2460
---------------------------------------------------------
Now when I run the grompp command it gives me following error:
ERROR 1 [file ffoplsaanb_lipid.itp, line 852]:
Invalid directive pair types
It's one word, pairtypes.
WARNING 1 [file ffoplsaanb_lipid.itp, line 854]:
Too few parameters on line (source file toppush.c, line 246)
Fix the above problem and the subsequent warnings should go away. grompp is
trying to interpret your pairtypes as atomtypes, since "pair types" was an
unrecognized directive.
-Justin
-----
Generated 359128 of the 359128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 359128 of the 359128 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'POPC'
There were 91 warnings
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1372
Fatal error:
There was 1 error in input file(s)
I am not able to get where I am going wrong.
Thanking you,
Parul
--
========================================
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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