RE: [gmx-users] Residue abbreviation list with explanations
And what is my current issue is? What should I replace the residue name with? Dallas B. Warren [EMAIL PROTECTED] wrote:Could you please help me to find a Residue abbreviation list web site. If you want to find out what people are calling a particular molecule or residue, best place to look is the PDB Database. If it is a small molecule, then http://alpha2.bmc.uu.se/hicup/ is a good place to look. However, as indicated previously, this is not what your current issue is. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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 - Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games.___ 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] Residue abbreviation list with explanations
And this is what I found there: see if there is a different name being used for the residue in the residue database and rename as appropriate, Mark Abraham [EMAIL PROTECTED] wrote: Sagittarius wrote: Dear Gromacs users, Could you please help me to find a Residue abbreviation list web site. I need to replace UNK below with something meaningful. formaldehyde.pdb looks like this: COMPND UNNAMED REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers REMARK 1 pertain to the .dat file from which this file was created, REMARK 1 not to one created from this file: REMARK 1 PDB: 1 2 3 4 REMARK 1 MMOD: 1 2 3 4 / HETATM 1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0 HETATM 2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0 HETATM 3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0 HETATM 4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0 CONECT 1 3 4 CONECT 1 2 CONECT 1 2 CONECT 2 1 CONECT 2 1 CONECT 3 1 CONECT 4 1 END Um no, you don't need a residue abbreviation list. See http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database Mark ___ 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 - Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out.___ 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] Residue abbreviation list with explanations
And what is my current issue is? What should I replace the residue name with? Ultimately, what ever you want to. From the name of the file, it seems like it is formaldehyde, which is a small molecule, and from the link I provide you the residue name used for it is FLH. So, convention wise, that is probably the best name to use for it. But, that is not going to solve your problem, since you are attempting to use pdb2gmx to generate your topology. And that is not going to work because FLH will not be in the residue database, as is noted at the link that was provided to you (http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in _residue_topology_database) I would suggest you actually READ what is at URL above. Funny enough, on the second line it actually mentions formaldehyde, take note of what it actually says. Plus also take notice of the second paragraph. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] Residue abbreviation list with explanations
Dear Gromacs users, Could you please help me to find a Residue abbreviation list web site. I need to replace UNK below with something meaningful. formaldehyde.pdb looks like this: COMPNDUNNAMED REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers REMARK 1 pertain to the .dat file from which this file was created, REMARK 1 not to one created from this file: REMARK 1 PDB: 1 2 3 4 REMARK 1 MMOD: 1 2 3 4 / HETATM1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0 HETATM2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0 HETATM3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0 HETATM4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0 CONECT134 CONECT12 CONECT12 CONECT21 CONECT21 CONECT31 CONECT41 END Thank you in advance - Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center.___ 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] Residue abbreviation list with explanations
Sagittarius wrote: Dear Gromacs users, Could you please help me to find a Residue abbreviation list web site. I need to replace UNK below with something meaningful. formaldehyde.pdb looks like this: COMPNDUNNAMED REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers REMARK 1 pertain to the .dat file from which this file was created, REMARK 1 not to one created from this file: REMARK 1 PDB: 1 2 3 4 REMARK 1 MMOD: 1 2 3 4 / HETATM1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0 HETATM2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0 HETATM3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0 HETATM4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0 CONECT134 CONECT12 CONECT12 CONECT21 CONECT21 CONECT31 CONECT41 END Um no, you don't need a residue abbreviation list. See http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database Mark ___ 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] Residue abbreviation list with explanations
Could you please help me to find a Residue abbreviation list web site. If you want to find out what people are calling a particular molecule or residue, best place to look is the PDB Database. If it is a small molecule, then http://alpha2.bmc.uu.se/hicup/ is a good place to look. However, as indicated previously, this is not what your current issue is. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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
