AMBER Archive (2004)

Subject: Re: AMBER: rdparm/ptraj writeparm + leap problem

From: david.evans_at_ulsop.ac.uk
Date: Wed Mar 17 2004 - 03:36:51 CST

Thanks for your help Tom.
I've managed to get it working most simply by just going back to the original leap.in file that I used to build the solvated system, and removing the ligand from there before writing a new prmtop file.

To do this I had to delete first the atoms of the ligand (residue SG)
remove complex complex.SG.34
.....
remove complex complex.SG.108

then the residue itself
remove complex complex.SG

Leap (both xleap and tleap) were seg faulting if I attempted just one of the above two steps.
I'm only posting this in case anyone wants to do the same as me in future, or if any developers are curious about leap bugs.

Dave Evans
London School of Pharmacy

---- Message from "Thomas E. Cheatham, III" <cheatham_at_chpc.utah.edu> at 2004-03-16 10:04:47 ------
>
>> I'm trying to use ptraj and rdparm to strip some atoms out of a
>> trajectory, and then output a prmtop file which corresponds to the
>> edited coordinates. I start 'rdparm prmtop.complex' and type
>>
>> >ptraj ptraj_water.in
>> >writeparm prmtop.water
>> >quit
>
>The "writeparm" command is part of the rdparm functionality and knows
>nothing of what happens in the ptraj part. In other words, the prmtop is
>not affected by the strip command.
>
>At present, your best option is to use tleap to read in a PDB and create a
>new prmtop that corresponds to the stripped trajectory. I would run ptraj
>again doing
>
>trajin mdcrd.1 1 1 1
>trajout snap.pdb pdb
>strip :1-25
>
>and then load in snap.pdb.1 into tleap.
>
>There is a (undocumented) command in rdparm to strip some (but not ALL) of
>the waters. The "testwater" command will create a new prmtop file with
>any number of waters (> 0). The writeparm command is present to write
>modified prmtop files that are modified by the commands to deletebonds,
>deleteangles, deletedihedrals, ... Ideally in the future ptraj will have
>prmtop writing capability, however this is still on the wish list.
>
>--tom
>
>p.s. if you are having trouble with xleap crashing, try tleap; it should
>easily work to build the new prmtop based on reading of a PDB file. In
>your case, if you are stripping the solute (i.e. :1-25) and building a
>prmtop for just the solvent in a truncated octahedral geometry, you will
>need to load the pdb and then build the box information; this is normally
>done with the setbox command, however this will not work for truncated
>octahedron. For this, you need to play with solvateOct setting a small
>buffer and large closeness so that a box is built, but no water is added.
>Good luck!
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