Hi,
I think that when you remove residues from a UNIT in leap, the bonds
between the residues are not automatically removed (which is the case
when removing individual atoms). You need to first remove whichever
bonds are connecting those residues with the 'deletebond' command
prior to removing the residues themselves. You can easily see which
atoms in a residue are the "connect" atoms with the desc command, e.g.
> desc m.2
RESIDUE name: ALA
RESIDUE sequence number: 2
RESIDUE PDB sequence number: 2
Type: protein
Connection atoms:
Connect atom 0: A<N 1>
Connect atom 1: A<C 9>
-Dan
On Fri, Mar 22, 2013 at 9:59 AM, Ignacio J. General <ijgeneral.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Mar 22 2013 - 09:30:05 PDT
