Dear Amber users,
I am using tleap to generate the files I need for a thermodynamic
integration of a protein+RNA+ions+water system. For the van der Waals step
of TI, I need to build a system without the two terminals of RNA, but the
rest should be exactly the same. So it is an unphysical system. The problem
is that when I remove them in tleap, then it cannot generate the prmtop
file; it segfaults.
Here is what I am doing in tleap:
-----------------------------------------------------------------------------
source leaprc.ff10
loadamberparams frcmod.ionsjc_tip3p
loadamberparams magnesium.frcmod
loadamberprep magnesium.prep
C=loadpdb 1000_v0_l00.pdb
A= copy C
B= copy C
remove B B.802
remove B B.821
set A box {101.7367567 101.7367567 101.7367567}
set B box {101.7367567 101.7367567 101.7367567}
saveamberparm A WT-ions-WAT8.prmtop 1000_v0_l00.rst
saveamberparm B WT-ions-WAT8-no802.prmtop 1000_v1_l00.rst
quit
-----------------------------------------------------------------------------
I tried many variations of the above script, different order of commands,
removing the ions, etc., but nothing works. It always generates the files
for system A, but not for B. They are empty. The error message for the last
command is:
-----------------------------------------------------------------------------
> saveamberparm B WT-ions-WAT8-no802.prmtop
1000_v1_l00.rst
Checking Unit.
WARNING: There is a bond of 108.748183 angstroms between:
------- .R<G 820>.A<O3' 34> and �<`��
821>.s<367567 101.7367567
101.7367567} 62>
WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: OS - >
Building angle parameters.
Could not find angle parameter: CT - OS - >
Could not find angle parameter: OS - > - O2
/home/ijgeneral/Applications/amber12/bin/tleap: line 17: 1293 Segmentation
fault $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep
-I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
-I$AMBERHOME/dat/leap/cmd $*
-----------------------------------------------------------------------------
That warning with a bond of 108 A would certainly be a problem, but I have
no idea why it appears there. I don't have such a thing in my system. And
it doesn't exist when it generates the files for system A...
Any ideas? This happens with AmberTools12 and 1.5.
Thanks,
Ignacio
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Received on Fri Mar 22 2013 - 09:30:03 PDT
