AMBER Archive (2002)

Subject: (no subject)

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Oct 04 2002 - 19:12:44 CDT

Hi,

I am trying to correct a pdb structure in which I removed all the
hydrogens (I only have the heavy atoms). I have 6 residues (1 ARG and 5
LYS) that are missing heavy atoms and I tried to use crdgrow to add those
heavy atoms back. Then I was planning to protonate the correct structure
and after that to check it in LEaP.

The input file is a normal .pdb file. The prep file I am using I tried to
generate it by taking the arginine residue description from all_amino94.in
and save it into a separate file (see below).

so for example, to correct the arginine residues I used
crdgrow -i protein.pdb -o test.pdb -p arginine.prep

The same I tried with lysine.
There's no error message just a Segmentation fault and a core dump.

I've seen that there was a question about the use of crdgrow on amber
before, however I could not find the answer to it in the archive.

To my understanding the prep file used by crdgrow should have a format
similar to the ip.prepin in the manual at page74. Am I wrong?
And it should work without hydrogens in it as well, right?

If you have a better idea to do the correction I am looking for please let
me know. I did try to input the whole structure into Leap, and I know leap
corrects automatically for it but I do not know how to tell Leap not to
add as well Hydrogens. I want to see first that my structure is correct
from the point of view of heavy atoms. If I let Leap use the hydrogens
it's all getting messy.

Thanks in advance for your help,
Ioana

***********************arginine.prep****
    1 1 2

ARGININE
db94.dat
 ARG INT 1
 CORR OMIT DU BEG
   0.00000
   1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
   2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
   3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
   4 N N M 3 2 1 1.335 116.600 180.000 -0.34790
   5 H H E 4 3 2 1.010 119.800 0.000 0.27470
   6 CA CT M 4 3 2 1.449 121.900 180.000 -0.26370
   7 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00070
   8 CG CT 3 8 6 4 1.525 109.470 180.000 0.03900
   9 CD CT 3 11 8 6 1.525 109.470 180.000 0.04860
  10 NE N2 B 14 11 8 1.480 111.000 180.000 -0.52950
  11 CZ CA B 17 14 11 1.330 123.000 180.000 0.80760
  12 NH2 N2 B 19 17 14 1.330 118.000 180.000 -0.86270
  13 C C M 6 4 3 1.522 111.100 180.000 0.73410
  14 O O E 26 6 4 1.229 120.500 0.000 -0.58940

IMPROPER
 CA +M C O

DONE
STOP
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