AMBER Archive (2009)

Subject: [AMBER] Problem reading PDB file into XLEAP

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Thu Mar 26 2009 - 19:01:26 CDT

Amber Users,

 

After I loaded a DNA file (DDIRinmin.pdb) into Xleap (Amber Tools 1.2)
from Amber 9, it was solvated,

counterions were added and a new PDB file (IR_sol.pdb) was created. I
then edited the new file

in order to remove the last water molecule from the file using Xemacs
while keeping the same file

name. This edited file was then loaded into Xleap once again in order
to create .prmtop and .inpcrd

files, but none of the residues are being recognized in Xleap, as
indicated in the leap.log. And,

although .prmtop and .inpcrd files are created, these files do not
function properly when used with

sander.

 

I've attached the original PDB file (DDIRinmin.pdb), the edited PDB
output file (IR_sol.pdb)

and the leap.log I added a note in the log file to indicate at what
point in the log I edited the output

PDB file IR_sol.pdb: the line begins with ***>>>. The archives
indicate some problems when

atom or residue names are not justified properly or when unusual names
are being used. I'm not

able to see either type of problem, and there was no apparent problem
processing the initial PDB file

in Xleap.

 

If anyone has run into this problem before or can offer suggestions, I
would really appreciate any

help offered. Thanks.

 

Bob Hopkins




  • application/octet-stream attachment: leap.log

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