[gmx-users] Prot_prep_problem

[andrea spitaleri]

HI Pkmukher,
I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and ligand
too. However if you want to be sticked with gromos ff I do as follow:
1. prepare my system with -ignh option in pdb2gmx
2. run the simulation
3. use protonate over the pdb and the final trr in order to analyze for instance the violated NOE.
Skip last question, sorry :)

Regards

andrea

pkmukher wrote:
> Hello gromacs users,
> 
> 
>   I am facing a particular problem in the preparation of my
> protein.I have a NMR derived structure with hydrogens. To
> prepare my protein i thought of a two step procedure
> 1)stripping the protein of the hydrogens using -ignh and
> saving pdb output
> 2)submitting the pdb output file from stage 1 using the
> -inter flag to get my final .top .gro and .pdb files
> 
> I find that at the end of step 1 the pdb output is stripped
> of hydrogens.
> In the second stage I find that the .top file has the
> hydrogens listed (only polar hydrogens) but the pdb output
> is still without any hydrogens.
> 
> I want to follow the gromacs tutorial titled
> GROMACS Tutorial for Drug – Enzyme Complex.
> http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
> 
> here they have used a prepared protein pdb file while
> merging the ligand coordinates to form the final complex.
> 
> My questions are
> 
> 1) why the pdb file written in step two does not contain the
> hydrogens and how can i solve this issue?
> 
> 2) Is there any other way to prepare the ligand-protein
> complex without using the protein .pdb output?
> 
> 3) This is a slightly unrelated question. Could some body
> guide me to any tutorials etc where they have shown how to
> calculate gausssian charges for the ligand and then
> incorporate into the gromacs ligand file?
> 
> I can provide the protein structure file. I couldnt load it
> to the group mail because of size limitations
> 
> Thanking you in anticipation
> 
> Prasenjit Kumar Mukherjee
> Graduate Student
> Department of Medicinal Chemistry
> School of Pharmacy
> University of Mississippi
> USA
> 
> Cell   - 662 380 0146
> Office - 662 915 1286 
> 
> 
> 
> 
> 
> 
> 
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-- 
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------

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