<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Thankyou very much Tsjerk, indeed this was the problem. I am most relieved this was the solution.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">I had assumed the distance was an upper bound on the acceptable distance.</DIV>
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Tsjerk Wassenaar <tsjerkw@gmail.com><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Sent: Sunday, 29 June, 2008 5:50:22 PM<BR>Subject: Re: [gmx-users] specbond recognised but not built<BR><BR>Hi Grange,<BR><BR>It recognizes the possibility of having a bond between these atoms.<BR>That's where the distance matrix comes in. But if a bond were made,<BR>you'd have a statement right after the distance matrix saying<BR>something like "linking atom ... and atom ...". It doesn't happen, and<BR>the reason is the following (you might want to search "specbond" in<BR>the user list archives): You have set your distance at 0.2 nm. pdb2gmx<BR>checks whether the actual distance is within 10% of the distance<BR>specified. The actual distance is 0.134, which lies well under the<BR>target distance. Therefore it doesn't
make the bond. Try to set the<BR>bond length in specbond.dat between 0.13 and 0.14.<BR><BR>Hope it helps,<BR></DIV></DIV></div><br>
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