[gmx-users] TIP3 water problem

[nikolaev at spbau.ru]

Ok, but how to craft it? I tried adding line in the end:
TIP3         76
but that failed to the wrong residue type...


> 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
>> >>>
>> >>> ==================================================
>> >>> --
>> >>> Gromacs Users mailing list
>> >>>
>> >>> * Please search the archive at
>> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >>> posting!
>> >>>
>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>>
>> >>> * For (un)subscribe requests visit
>> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>> >>> send
>> >>> a mail to gmx-users-request at gromacs.org.
>> >>>
>> >>
>> >>
>> >
>> > --
>> > ==================================================
>> >
>> > 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
>> >
>> > ==================================================
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send
>> > a mail to gmx-users-request at gromacs.org.
>> >
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>