[gmx-users] TIP3 water problem

[Justin Lemkul]

On 12/25/16 8:01 AM, nikolaev at spbau.ru wrote:
> Ok, but how to craft it? I tried adding line in the end:
> TIP3         76
> but that failed to the wrong residue type...
>

Water is called "SOL" in GROMACS.  Always check the [moleculetype] name in the 
.itp file before hacking the system topology.

-Justin

>
>> Hi,
>>
>> That's fine, but you still don't need pdb2gmx to try to generate
>> topologies
>> for any kind of water. Use pdb2gmx to generate your protein itp file, and
>> then craft the top file to match the contents of the structure file that
>> e.g had crystallographic water before you solvated it also. The tools are
>> flexible and powerful, and not everything has to follow the simple linear
>> examples in tutorials :-)
>>
>> Mark
>>
>> On Sun, 25 Dec 2016 09:37 <nikolaev at spbau.ru> wrote:
>>
>>> Oh, sorry, these were only charges, masses etc, no coords.
>>> I wish I could use only gromacs waters, but I use extra software for
>>> prediction of crystallographic waters...
>>>
>>>
>>>>
>>>>
>>>> On 12/23/16 3:30 AM, nikolaev at spbau.ru wrote:
>>>>> Well, as I understand I need to do the following:
>>>>>
>>>>> Provide pdb file with different chains for protein and waters;
>>>>> gmx pdb2gmx -f 3WQJ.pdb -o 3wqj.gro
>>>>>
>>>>> then go into the topol_Other_chain_X.itp;
>>>>> delete everything that after the atom coords;
>>>>>
>>>>
>>>> There are no coordinates in any .itp file, so I don't follow.
>>>>
>>>>> then run everything in the same way.
>>>>>
>>>>> I have tried this and it seems to work, I just want to make sure that
>>> I
>>>>> am
>>>>> doing everything right.
>>>>>
>>>>
>>>> Basically, my recommendation is: don't feed waters to pdb2gmx.
>>> Solvate
>>>> with
>>>> normal GROMACS tools and use the stock water topology, which accounts
>>> for
>>>> everything.
>>>>
>>>> -Justin
>>>>
>>>>> Anyway, thank you for help!
>>>>>
>>>>> Dmitrii.
>>>>>
>>>>>
>>>>>>
>>>>>>
>>>>>> On 12/20/16 2:41 PM, nikolaev at spbau.ru wrote:
>>>>>>> Hi, all!
>>>>>>>
>>>>>>> I am working with the protein structure with internal waters of
>>> TIP3
>>>>>>> type,
>>>>>>> and running grompp ends with an error of "No default U-B types", as
>>> I
>>>>>>> understand because of some internal inconsistency between atom
>>> types
>>>>>>> (H1,
>>>>>>> H2 and OH2 in my tip3, HW1, HW2, OW in sol). I tried to rename
>>> atoms
>>>>>>> in
>>>>>>> both topol.top and .gro files, add extra .itp file in charmm27.ff,
>>>>>>> nothing
>>>>>>> worked.
>>>>>>>
>>>>>>> However, this problem has already been mentioned here:
>>>>>>>
>>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/087725.html
>>>>>>>
>>>>>>> and the solution involved modifying top file (add waters
>>> information
>>>>>>> manually). Is it really the only solution of this problem? Because
>>> as
>>>>>>> I
>>>>>>> understand I need to insert manually all the charges, angles, bond
>>>>>>> lenths
>>>>>>> for all the water molecules. And it seems quite a problem, if I
>>> want
>>>>>>> to
>>>>>>> run more than 1 system.
>>>>>>>
>>>>>>
>>>>>> Water molecules should not have [bonds] and [angles] directives
>>> because
>>>>>> they
>>>>>> should be treated as rigid via SETTLES.  If your topology has
>>> explicit
>>>>>> bonds and
>>>>>> angles, remove them and re-process the coordinates with pdb2gmx to
>>>>>> prevent
>>>>>> this
>>>>>> spurious assignment.  Then just #include "tip3p.itp" and list the
>>>>>> waters
>>>>>> in
>>>>>> [molecules].
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 629
>>>>>> 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 629
>>>> 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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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