[gmx-users] TIP3 water problem

[nikolaev at spbau.ru]

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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