On Tue, Apr 21, 2015, Vaibhav Dixit wrote:
>
> kmcdwlx005 462% tail P450_test.inpcrd
> 12.9410318 24.7763059 28.5292431 6.0666578 11.2373217 31.8421776
> 5.7263398 10.4381030 32.2442456 5.3605584 11.5374928 31.2698610
> 6.7183050 8.3222530 30.2949099 7.5409119 7.8483008 30.1727990
> 6.9621113 9.1013013 30.7947786 4.2421629 15.0141650 28.1041078
> 4.0966209 15.3281953 28.9965360 3.7646832 15.6326551 27.5511977
> 6.1018012 12.0044198 28.1521968 6.0879580 11.1085292 27.8154266
> 6.8190440 12.0114862 28.7860254 7.9544142 12.4381539 30.1975095
> 7.6961920 13.3598609 30.1959426 7.4229183 12.0411973 30.8875559
> 12.8990331 25.5432326 22.9765180 13.0727209 24.9778748 22.2239033
> 13.3919222 26.3433221 22.7944670 8.3746098 8.5713
This file looks truncated, as thought the the LEaP program did not correctly
complete, or there were a disk error, or something like that.
>
> My current leap.in
> ukmcdwlx005 463% more leap.in
> source leaprc.ff14SB
> source leaprc.gaff
> CYP = loadmol2 CYS_HS.mol2
> set CYP head CYP.1.N
> set CYP tail CYP.1.C
> desc CYP
> HEM = loadmol2 HEM_pentacoordinateHS.mol2
> loadamberparams HEM_HS.frcmod
> loadamberparams frcmod.ionsjc_tip3p
> P450 = loadpdb 1W0E_P450_leap.pdb
> bond P450.419.SG P450.477.FE
> solvateoct P450 TIP3PBOX 12
> charge P450
> addions P450 Cl- 0
>
I'll assume(?) you had a saveAmberParm command somewhere, and decided not
to let us see it. Check the leap.log file for errors. Try re-running the
script. Now that you know to run "tail" on the inpcrd file, you can start
to debug the problem. Check both the output that comes to stdout, and the
info in leap.log to try to find out what is going on.
...good luck....dac
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Received on Tue Apr 21 2015 - 08:30:04 PDT
