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

[Justin Lemkul]

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.

-Justin

>
>
>
> On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/3/14, 10:57 AM, gromacs query wrote:
>>
>>> Hi All
>>>
>>> I am trying to use charmm36 (charmm36-jan2014 from charmm website) with
>>> popc membrane built using charmm-gui (have water and ions).
>>>
>>> I used commands as follows:
>>>
>>> pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff
>>> charmm36-jan2014
>>> editconf -f popc.gro -o popc_box.gro -c -d 0.0
>>> grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr
>>>
>>> I get this error: (so many)
>>> ERROR 11520 [file topol.top, line 184419]:
>>>     No default U-B types
>>>
>>> Where are UB for charmm36?
>>>
>>>
>> This shouldn't happen.  Can you please identify what atoms are causing the
>> failure?  It may help to simplify by working only with a single lipid
>> rather than a full membrane.
>>
>> -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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-- 
==================================================

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

==================================================