[gmx-users] No default U-B types charmm
jalemkul at vt.edu
Mon Mar 3 19:38:04 CET 2014
On 3/3/14, 1:34 PM, Justin Lemkul wrote:
> On 3/3/14, 1:25 PM, gromacs query wrote:
>> Hi Justin
>> Its problem with the waters I think. I found conflict in water atom names:
>> 1 OT 1 SOL OW 1 -0.834
>> 2 HT 1 SOL HW1 1 0.417
>> 3 HT 1 SOL HW2 1 0.417
>> [ TIP3 ]
>> [ atoms ]
>> OH2 OT -0.834 0
>> H1 HT 0.417 1
>> H2 HT 0.417 2
>> In PDB from charmgui its OH2,H1,H2. I changed names in
>> charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same error.
> That's not the problem. Waters don't have dihedrals. Naming mismatches are a
> simple thing to solve and would raise a different (non-serious) error.
Retracted. For some reason my brain made U-B into R-B. Waters held rigid by
SETTLE do not have U-B parameters. I would suggest simply #including tip3p.itp
rather than have waters explicitly within any other [moleculetype] with their
own [angles] directive. The names themselves are still not a problem; it is the
fact that a rigid water model is now having U-B incorrectly added, which is what
pdb2gmx does by default (and is not always right).
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
More information about the gromacs.org_gmx-users