<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Mark,</span></div><div><br><span></span></div><div><span>It seems you do not work in a molecular dynamics simulation lab, but you are very interested in molecular dynamics simulation, including having answered one of my questions before. Can you explain the reason to me?</span></div><div><br><span></span></div><div><span>Dialing</span></div><div><br></div> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span
style="font-weight: bold;">Sent:</span></b> Friday, 17 February 2012 10:44 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] NME not found in rtp<br> </font> </div> <br>On 17/02/2012 10:27 PM, francesca vitalini wrote:<br>> Hi all!<br>> I encounter this error while running pdb2gmx on GROMACS3.3.1 with<br>> ffG53a6m il forcefield modificato per la reverse transformation.<br>><br>> Fatal error:<br>> Residue 'NME' not found in residue topology database<br>><br>> I know I should add it to the .rtp file, but I don't know exactly how<br>> to do that, any help?<br><br>Check the .rtp in case it has this residue under a different name (often <br>NAC). Otherwise, you need to check out the relevant part of chapter 5 of <br>the manual, and proceed by analogy from the other C-terminal capping <br>residues that are there.<br><br>Mark<br><br>> Otherwise, I'm actually just looking for a toy system with which
just<br>> play around as I'm having issues with the reverse transformation. Any<br>> suggestion for a pdb? thanks!<br>><br>><br>><br><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists"
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