[gmx-users] TIP3 water problem
nikolaev at spbau.ru
nikolaev at spbau.ru
Fri Dec 23 09:39:55 CET 2016
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!
> 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
>> and running grompp ends with an error of "No default U-B types", as I
>> understand because of some internal inconsistency between atom types
>> 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,
>> However, this problem has already been mentioned here:
>> 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
>> 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
> 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
> spurious assignment. Then just #include "tip3p.itp" and list the waters
> 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
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