[gmx-users] Prot_prep_problem

andrea spitaleri spitaleri.andrea at hsr.it
Wed Apr 11 16:56:46 CEST 2007

I apology for the incorrect spelling of your name ...
I have an automatic reply format which sometimes does weird stuff ...
Sorry  Prasenjit, really.



andrea spitaleri wrote:
> 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)

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