Hi,<br><br>I have three problems with pdb2gmx. They are all related to the n-terminus patch I use for cellulose.<br><br>The patch is:<br>[ replace ]<br>C4 CTS 12.01100 0.14<br>H4 HAS 1.00800 0.09<br>
[ add ]<br>1 2 O4 C4 C5 C6<br> OHS 15.99940 -0.660<br>1 2 HO4 O4 C4 C5<br> HOS 1.00800 0.430<br>[ bonds ]<br>O4 C4<br><br>The problems are:<br>
<br>1)<br><br>I add two atoms in the N Terminus Patch like this:<br><br>Still pdb2gmx compalns: <br>Fatal error:<br>Atom O4 in residue BGLC 1 not found in rtp entry with 21 atoms<br>
while sorting atoms<br><br>It works without problem with -nosort option. The problem is that the function sort_pdbatoms is called by pdb2gmx before the patches are applied.<br>IMHO the reason this is no problem for a protein is that the additional atoms are renamed using xlateat.dat so that they are known even before the patches are applied. <br clear="all">
<br><br>2) <br>The charge and charge group number of two hydrogen atoms get changed even though they are not part of the patch at all.<br><br>The residue is:<br>
[ BGLC ]<br>
[ atoms ]<br>
C1 CBS 0.3 1<br>
H1 HAS 0.1 1<br>
O1 OES -0.4 1<br>
C5 CTS 0.1 1<br>
H5 HAS 0.1 1<br>
O5 OES -0.4 1<br>
C4 CTS 0.1 1<br>
H4 HAS 0.1 1<br>
C2 CTS 0.140 2<br>
<b>H2 HAS 0.090 2</b><br>
O2 OHS -0.660 2<br>
HO2 HOS 0.430 2<br>
C3 CTS 0.140 3<br>
<b> H3 HAS 0.090 3</b><br>
O3 OHS -0.660 3<br>
HO3 HOS 0.430 3<br>
C6 CPS 0.050 4<br>
H61 HAS 0.090 4<br>
H62 HAS 0.090 4<br>
O6 OHS -0.660 4<br>
HO6 HOS 0.430 4<br><br>but after the patch the charge and charge group numbers of H2 and H3 are:<br> 1 CTS 1 BGLC C5 1 0.1 12.011 ; qtot 0.1<br> 2 HAS 1 BGLC H5 1 0.1 1.008 ; qtot 0.2<br>
3 OES 1 BGLC O5 1 -0.4 15.9994 ; qtot -0.2<br> 4 HAS 1 BGLC H1 1 0.1 1.008 ; qtot -0.1<br> 5 CBS 1 BGLC C1 1 0.3 12.011 ; qtot 0.2<br>
6 OES 1 BGLC O1 1 -0.4 15.9994 ; qtot -0.2<br> 7 CTS 1 BGLC C2 2 0.14 12.011 ; qtot -0.06<br> 8 HAS 1 BGLC <b> H2 3 0.1</b> 1.008 ; qtot 0.04<br>
9 OHS 1 BGLC O2 4 -0.66 15.9994 ; qtot -0.62<br> 10 HOS 1 BGLC HO2 4 0.43 1.008 ; qtot -0.19<br> 11 CTS 1 BGLC C3 5 0.14 12.011 ; qtot -0.05<br>
12 HAS 1 BGLC <b>H3 6 0.1</b> 1.008 ; qtot 0.05<br> 13 OHS 1 BGLC O3 7 -0.66 15.9994 ; qtot -0.61<br> 14 HOS 1 BGLC HO3 7 0.43 1.008 ; qtot -0.18<br>
15 CTS 1 BGLC C4 8 0.14 12.011 ; qtot -0.04<br> 16 HAS 1 BGLC H4 8 0.09 1.008 ; qtot 0.05<br> 17 OHS 1 BGLC O4 8 -0.66 15.9994 ; qtot -0.61<br>
18 HOS 1 BGLC HO4 8 0.43 1.008 ; qtot -0.18<br> 19 CPS 1 BGLC C6 9 0.05 12.011 ; qtot -0.13<br> 20 HAS 1 BGLC H61 9 0.09 1.008 ; qtot -0.04<br>
21 HAS 1 BGLC H62 9 0.09 1.008 ; qtot 0.05<br> 22 OHS 1 BGLC O6 9 -0.66 15.9994 ; qtot -0.61<br> 23 HOS 1 BGLC HO6 9 0.43 1.008 ; qtot -0.18<br>
<br>The charges and charge groups are correct for all but the first residue. So for all residues for which the n-terminus patch is not applied.<br><br>3)<br>The above add of two atoms misses one bond. I need to specify manually to add the bond (as shown above):<br>
[ bonds ]<br>O4 C4<br><br><br>Non of the problems is very severe, because I have a workaround for 1 and 3 and I can manually change 2. But I wanted to report the problems.<br>Roland<br><br><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>