[gmx-users] No default U-B types charmm

[Justin Lemkul]

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:
>>
>> charmm36-jan2014.ff/tip3p.itp:
>> 1       OT      1       SOL              OW             1       -0.834
>> 2       HT      1       SOL             HW1             1        0.417
>> 3       HT      1       SOL             HW2             1        0.417
>>
>>
>>
>> charmm36-jan2014.ff/merged.itp
>> [ 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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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