Thanks Jason for the reply. Sorry that I missed the email from the mailing
list.
It recycles after 999 because in the prmtop file, the residue labels are
written in the format of a4, and I assume the last character of the four
should be space as separation.
R0 R1 R2 R3 R4 R5 R6 R7 R8 R9 R10 R11 R12 R13 R14 R15 R16 R17 R18
R19
...
980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998
999
000 001 002 003 004 005 006 007 008 009 010 011 012 013 014 015 016 017 018
019
...
I started to run some simple equilibrations of the system. It didn't seem to
cause problems yet, but I am not sure.
Sincerely,
Pengzhi
On Thu, Aug 28, 2014 at 3:36 PM, Pengzhi Zhang <zhangpengzhi1988.gmail.com>
wrote:
> Dear AMBER users,
>
> I use coarse-grained protein model (each residue has 2 beads) and run
> with modified version of AMBER10. I am trying to build the prmtop file
> for a system with ~5000 residues, I notice that in the prmtop file the
> residue label runs out up to 999 and recycle again ... Does this will
> cause a problem in sander?
>
> Any comments and suggestions are appreciated!
>
?It might cause a problem. Why does the residue number recycle after 999?
?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 02 2014 - 15:00:02 PDT
