Daniel, yes, that was the problem. Solved just deleting the bond, as you
said. Thanks so much!
Ignacio
On Fri, Mar 22, 2013 at 12:15 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Mar 22 2013 - 10:30:02 PDT
