Dear Amber users:
I am using amber 9 and want to cap the N and C terminal for the given
protein.
So, in the given protein the first residue at position 1 and the last one at
position 149 were modified by adding ACE and NME groups.
ATOM 1 C ACE A 1 70.110 65.868 39.946 1.00 0.00
ATOM 2 CA ALA A 1 70.537 66.473 38.657 1.00 0.00
ATOM 3 C ALA A 1 69.639 67.664 38.316 1.00 0.00
ATOM 4 O ALA A 1 68.434 67.654 38.604 1.00 0.00
ATOM 5 CB ALA A 1 70.456 65.436 37.551 1.00 0.00
ATOM 6 N THR A 2 70.232 68.687 37.711 1.00 0.00
ATOM 7 CA THR A 2 69.495 69.875 37.320 1.00 0.00
ATOM 8 C THR A 2 69.540 70.004 35.797 1.00 0.00
.
.
.
ATOM 1182 CA HID A 149 72.111 68.499 32.373 1.00 0.00
ATOM 1183 C HID A 149 73.534 68.060 32.700 1.00 0.00
ATOM 1184 O HID A 149 74.355 67.976 31.762 1.00 0.00
ATOM 1185 CB HID A 149 71.171 67.340 32.690 1.00 0.00
ATOM 1186 CG HID A 149 71.681 66.008 32.234 1.00 0.00
ATOM 1187 ND1 HID A 149 71.796 65.669 30.903 1.00 0.00
ATOM 1188 CD2 HID A 149 72.104 64.928 32.935 1.00 0.00
ATOM 1189 CE1 HID A 149 72.263 64.437 30.803 1.00 0.00
ATOM 1190 N NME A 149 72.457 63.965 32.021 1.00 0.00
Also, here below is the input file, sander.in_leo, for ironing out the poor
placemats of these two gropes.
min + md
&cntrl imin = 1, irest=0, ibelly=1,
ntx=1, idiel = 0, cut = 8.0, SCEE=1.2,
ntpr=500, maxcyc=20000, ncyc=8000, drms=0.01
&end
Group input for restrained atoms
50.0
RES 1
RES 151
END
END
Finally, here comes the error messages like this:
forrtl: severe (19): invalid reference to variable in NAMELIST input, unit
5, file
/mount/disk15/backy/system/RNA/Amber/RNA_bound/Backy/cap-1jbs-A-GB/sander.in_leo,
line 3, position 14
Image PC Routine Line Source
sander 08560280 Unknown Unknown Unknown
sander 0855FD78 Unknown Unknown Unknown
sander 0852D0D9 Unknown Unknown Unknown
sander 084F098C Unknown Unknown Unknown
sander 084F0E2F Unknown Unknown Unknown
sander 0850E440 Unknown Unknown Unknown
sander 080E96B2 Unknown Unknown Unknown
sander 080D040C Unknown Unknown Unknown
sander 080D0155 Unknown Unknown Unknown
sander 0804A5E8 Unknown Unknown Unknown
Unknown 006BBDE3 Unknown Unknown Unknown
sander 0804A4A1 Unknown Unknown Unknown
Could anyone figure what's wrong?
Thanks.
backy
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Received on Sun Jun 24 2007 - 06:07:04 PDT
