[gmx-users] lipid.itp with gromacs3.1.4
vincent.lemaitre at bioch.ox.ac.uk
Wed Oct 30 12:50:48 CET 2002
This has already been discussed on the mailing list... search using
lipid and Tieleman as key words.
Marc Baaden's warning about the somewhat unexpected behavior of grompp
having multiple atomtypes and non-bonded entries applies to using
too. In the way I set it up, the LJ interaction matrix in the GROMOS
force fields (ffgmx in this case) is overwritten with standard
rules. I don't yet know what the effect is of this. It means the force
isn't used the way it was designed. On the other hand, nearly all
simulations on membrane proteins with gromacs will have used the
rules for the protein part instead of the GROMOS values, often without
To use the protein-protein GROMOS LJ parameters, the contents of
should be copied into the ffgmx* files as Marc described. It should be
possible to test the differences on simulations of high-resolution
Dr. D.P. Tieleman, Assistant Professor, AHFMR Scholar
Department of Biological Sciences, University of Calgary
2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
web: www.ucalgary.ca/~tieleman fax: (403)289-9311 tel: (403)220-2966
On Mercredi, octobre 30, 2002, at 05:38 , Xu Yong wrote:
> hi, all
> Does anyone use Gromacs-3.1.4 to do some lipid/protein simulation?
> When I do grompp with only popc128a.pdb system, I encounter a Fatal
> error: Found a second directive: ./lipid.itp line 9.
> this line is the first line of lipid [ atomtypes ] option :
> "LO *** ** ** A *** *** OPLS"
> Does anyone encounter the same problem, and how to solve it? Would you
> like give me the system.top, lipid.itp, ffgmx.itp ffgmxnb.itp and
> ffgmxbon.itp files? which files should be included and which lines
> should be deleted.
> any reply would be appreciated!
> Best Regard
> Xu Yong
> Center for Drug Discovery & Design
> State Key Laboratory of Drug Research
> Shanghai Institute of Materia Medica
> Chinese Academy of Sciences
> 294, Taiyuan Road
> Shanghai 200031
> People's Republic of China
> E-mail: yxu at mail.shcnc.ac.cn
> & yxu at iris3.simm.ac.cn
> Phone: 86-21-64311833-615/222(L)
> Fax: 86-21-64318401
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users