one of your namelist variables is wrong, usually it is easiest
to find this by removing them one by one until it runs, then you
know which one was incorrect. in this case it might be that idiel is not
a sander variable.
On 6/20/07, backy <backy.ibms.sinica.edu.tw> wrote:
>
> 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 - 06:07:05 PDT
