Re: [gmx-users] Prot_prep_problem
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 listgmx-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]
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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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Re: [gmx-users] Prot_prep_problem
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 listgmx-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 listgmx-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]
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[gmx-users] Prot_prep_problem
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 listgmx-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
Re: [gmx-users] Prot_prep_problem
pkmukher wrote: Hello group users, I am trying to prepare a protein using the pdb2gmx module of gromacs.I have stripped the hydrogens using a different program and using a pdb file as the input.I am getting the following error message. Please help me with your suggestions on this. Thank you kindly. Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Number of bonds was 1726, now 1723 Generating angles, dihedrals and pairs... Before cleaning: 2697 pairs --- Program pdb2gmx, VERSION 3.3.1 Source code file: pgutil.c, line: 87 Fatal error: Atom N not found in residue 1 while adding improper So, is there an N atom in your first residue? -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
[gmx-users] Prot_prep_problem
Hello group users, I am trying to prepare a protein using the pdb2gmx module of gromacs.I have stripped the hydrogens using a different program and using a pdb file as the input.I am getting the following error message. Please help me with your suggestions on this. Thank you kindly. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges 10: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Reading 1YSI_orient_chop2_protein_noH.pdb... Read 1307 atoms Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 163 residues with 1307 atoms chain #res #atoms 1 'A' 163 1307 All occupancies are one Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1.atp Atomtype 50 Reading residue database... (ffG43a1) Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1.rtp Residue 96 Sorting it all out... Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1.hdb Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1-n.tdb Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1-c.tdb Back Off! I just backed up j.top to ./#j.top.1# Processing chain 1 'A' (1307 atoms, 163 residues) There are 247 donors and 258 acceptors There are 294 hydrogen bonds Will use HISB for residue 77 Will use HISB for residue 141 Checking for duplicate atoms Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully N-terminus: NH3+ C-terminus: COO- Now there are 163 residues with 1693 atoms Making bonds... Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Number of bonds was 1726, now 1723 Generating angles, dihedrals and pairs... Before cleaning: 2697 pairs --- Program pdb2gmx, VERSION 3.3.1 Source code file: pgutil.c, line: 87 Fatal error: Atom N not found in residue 1 while adding improper --- "Torture You Yeah, That's a Good Idea, I Like That." (Pulp Fiction) 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 listgmx-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
