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

[Justin Lemkul]

On 3/3/14, 3:56 PM, gromacs query wrote:
>>> What atom numbers are on line 184419? What atom types are they in the
> [atoms] section for that [moleculetype]?
>
> These are waters only (I am using tipS3p CHARMM TIP3P). UB should not be
> there. I am following Justin's suggestion to remove moleculetype from top
> file (still not solved and trying, will let you know; I am newbie to
> gromacs)
>

Hopefully you're not removing entire [moleculetype] directives, that would be 
rather horrible.

The proper solution is to not process waters with pdb2gmx.  You can hack the 
topology to fix it, but the best bet is to strip waters, process with pdb2gmx to 
get a topology for everything that's not water, then add back the water 
coordinates from the original coordinate file and adjust [molecules] 
accordingly.  If you are very new to Gromacs, invest some time working with 
tutorials simple systems to familiarize yourself with the format before doing 
these manipulations.  In the long run, it will save you time and mistakes.

-Justin

> thanks
>
>
> On Mon, Mar 3, 2014 at 6:48 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> On Mon, Mar 3, 2014 at 7:25 PM, gromacs query <gromacsquery at gmail.com
>>> wrote:
>>
>>> Hi Justin
>>>
>>> Its problem with the waters I think.
>>
>>
>> Can't be, they have no U-B.
>>
>>
>>> 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.
>>>
>>>
>>>
>>>
>>> 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
>>>
>>
>> What atom numbers are on line 184419? What atom types are they in the
>> [atoms] section for that [moleculetype]?
>>
>> Mark
>>
>>
>>>>>
>>>>> 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

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