I apology for the incorrect spelling of your name ... I have an automatic reply format which sometimes does weird stuff ... Sorry Prasenjit, really.
Regards andrea 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 >> >> >> >> >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php