[gmx-users] No default U-B types charmm
gromacs query
gromacsquery at gmail.com
Wed Mar 5 20:04:28 CET 2014
Hi Justin and Mark
>> 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
It worked Thanks. So in brief it goes like this:
1) build membrane with CHARMMgui
2) Remove ions and water from CHARMMGUI pdb and save just the membrane pdb.
Use this pdb with pdb2gmx to get top file (I used charmm36)
3) Modify [molecules] in top file (add ions and waters information manually)
JIom
On Mon, Mar 3, 2014 at 9:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
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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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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>
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