FYI, I only showed you the bond part of the residue in the previous email
(since that was the section I was commenting on and showed how it should be
there) there should be some atom details prior to that, as required by the rtp
format. You need to use your own judgment and the manual to
As noted by your rtp entry:
[ bonds ]
C1-C4
C1H11
C1H12
C1C2
C2F21
C2F22
C2+C3
C3F31
C3F32
C3C4
C4F4
C4Cl4
C4+C1
One end of the residue bonds via the C1 to a C4 in the next
That is something you will have to sort out, since you have all the files (in
and out) and know the molecule(s) you are processing. You have provided
insufficient information to help without having to spend a significant amount
of time trying to work what it all means.
If pdb2gmx is telling
Have you done it with polymer chain of length 1, one FRE, with the end methyl
groups capping it off, FBG and FEN? Does that work?
Sounds bit like the RTP entry is not set up correctly.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash
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