[gmx-users] TIP3 water problem

[nikolaev at spbau.ru]

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;

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.

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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