[gmx-users] Prot_prep_problem

[pkmukher]

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