I want to simulate a protein that has an ion (Mg+) and a GDP molecule. As we know Gromacs can't identify the GDP molecule that's why I got the topology and saved it as gdp.itp in the same directory + also added it in .top file.
However, after the completion of every step, when I check the output file, the GDP is gone.
Interesting part is that I get no error.
I tried various ways to cope with it but all in vain.
[There are different parameters for GDP, GTP, NADH and NADPH etc for AMBER but in case of Gromacs I couldn't found anything like this+I don't know how and from where to get the .rtp file for my force field (OPLS) as adding my residue to it may work for me]
Kindly enlighten us.
Thanks
It would be helpful if you could explain, where the problems appeared for the first time. No error by pdb2gmx, no error by grompp, no error by mdrun?
Was the GDP molecule part of your structure file (*gro or *pdb)?
Did it have the same residuename as in the topology?
The GDP is included in the .pdb file but as Gromacs can't recognize it, that's why first I removed the GDP from the .pdb structure and generated the topology only for the protein along with its Mg ion. After the generation of topology, I used an online server PRODRG to generate topology for the GDP and saved it in the same directory as gdp.itp. Also I added the GDP coordinates to the .gro file and mentioned it in the .top file.
The next step is to add water.
So I used the following command!
gmx editconf -f kw_processed.gro -o newbox.gro -bt cubic -d 2.5
But the output that I received from the above command lacks the GDP which is surprising.
[Screen shots are given to better understand the situation]
Michal H. Kolář Stéphane Abel
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