Hi all,<br><br>I currently mix GLYCAM and AMBER in gromacs4.0.7 using the amberports and <a href="http://amb2gmx.pl">amb2gmx.pl</a> 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.<br>
<br>From Glycam_06g.dat:<br>"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 <br>
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."<br><br>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. <br>
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.<br>
<br>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: <br>
<a href="http://dev-archive.ambermd.org/200812/0000.html">http://dev-archive.ambermd.org/200812/0000.html</a><br><br>The relevant part being:<br>"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."<br><br>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.<br>
<br>Thanks,<br><br>Oliver<br> <br><br>