[gmx-users] lipid.itp with gromacs3.1.4

[Vincent Lemaitre]

Hi Xu,

This has already been discussed on the mailing list... search using 
lipid and Tieleman as key words.

Hi all,

Marc Baaden's warning about the somewhat unexpected behavior of grompp 
when
having multiple atomtypes and non-bonded entries applies to using 
lipid.itp
too. In the way I set it up, the LJ interaction matrix in the GROMOS 
based
force fields (ffgmx in this case) is overwritten with standard 
combination
rules. I don't yet know what the effect is of this. It means the force 
field
isn't used the way it was designed. On the other hand, nearly all 
published
simulations on membrane proteins with gromacs will have used the 
combination
rules for the protein part instead of the GROMOS values, often without
disastrous consequences.

To use the protein-protein GROMOS LJ parameters, the contents of 
lipid.itp
should be copied into the ffgmx* files as Marc described. It should be
possible to test the differences on simulations of high-resolution 
membrane
protein structures.

Peter

--
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
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>  People's Republic of China
>  E-mail: yxu at mail.shcnc.ac.cn
>        & yxu at iris3.simm.ac.cn
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