Hi all, I currently mix GLYCAM and AMBER in gromacs4.0.7 using the amberports and amb2gmx.pl for the glycan. My problem is that I can't mix the scaling properly as required for correct rotamer population sampling of the glycan with the protein present.
>From Glycam_06g.dat: "Correct rotational behavior for O-C-C-O fragments requires SCEE=SCNB=1.0. This is in contrast to "standard" AMBER, in which it is normal to set SCEE=1.2 and SCNB=2.0. Unless you are attempting to generate rotamer populations, it is OK to use the "standard" values. Using non-standard values (SCEE=SCNB=1.0) may be unacceptable when a protein is also present." So in gromacs GLYCAM requires a fudgeQQ = 1.0 and a fudgeLJ = 1.0 whereas the ffamberports requires fudgeQQ = 0.8333 and a fudgeLJ = 0.5. I've been reading the mailing list archive and chris neale's method from 2006 for combining the Berger lipids and OPLS-AA forcefields however, as he states, the method won't work in this case as the ratio of the fudgeQQ factors is not an integer. My understanding was that it is not possible at the minute to do this correctly in gromacs. It would require a [ pairtypes ] section for 1-4 coulomb interactions. However I found this discussion from 2008: http://dev-archive.ambermd.org/200812/0000.html The relevant part being: "we're chatting about implementing mixed 1-4 scaling in gromacs. It's easy to enable on a per-molecule basis. Enabling on a per-residue and per-atom basis is certainly possible, but there are a bunch of ways to do it." So... Is it currently possible to implement mixed 1-4 scaling on a per-molecule basis? I've checked the 4.5.3 manual but it seems not to have changed since 4. Thanks, Oliver
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