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

[gromacs query]

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.




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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