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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hello,<br>
Am anik. Am using gromacs 4.5.5<br>
I could not find the proper reason of the foillowig failure of my job. please help.<br>
<br>
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<span style="font-weight:bold">The following is a part of the dna pdb file, which I am using:</span><br>
<br>
ATOM 1 OH DG5 X 1 13.663 36.760 21.465 0.00 0.00 <br>
ATOM 2 CT DG5 X 1 14.791 36.040 21.150 0.00 0.00 <br>
ATOM 3 CT DG5 X 1 14.771 34.703 21.873 0.00 0.00 <br>
ATOM 4 OS DG5 X 1 16.017 34.553 22.577 0.00 0.00 <br>
ATOM 5 CT DG5 X 1 13.724 34.528 22.970 0.00 0.00 <br>
ATOM 6 OS DG5 X 1 13.540 33.118 23.234 0.00 0.00 <br>
............................................................................................<br>
<br style="font-weight:bold">
<span style="font-weight:bold">I am using amber 03 forcefield (amber03.ff) whose atom type is as follows:</span><br>
<br>
H0 1.00800 ; H aliph. bond. to C with 1 electrwd. group (03GLY)<br>
Br 79.90000 ; bromine<br>
C 12.01000 ; sp2 C carbonyl group <br>
CA 12.01000 ; sp2 C pure aromatic (benzene)<br>
CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction<br>
CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS<br>
CK 12.01000 ; sp2 C 5 memb.ring in purines<br>
CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6<br>
..................................................................................................<br>
<br>
<br style="font-weight:bold">
<span style="font-weight:bold">The dna-rtp file in the amber 03 is as follows:</span><br>
<br>
[ bondedtypes ]<br>
; Col 1: Type of bond<br>
; Col 2: Type of angles<br>
; Col 3: Type of proper dihedrals<br>
; Col 4: Type of improper dihedrals<br>
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.<br>
; Col 6: Number of excluded neighbors for nonbonded interactions<br>
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1<br>
; Col 8: Remove impropers over the same bond as a proper if it is 1<br>
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih<br>
1 1 9 4 1 3 1 0<br>
<br>
<br>
; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's <br>
<br>
[ DA5 ]<br>
[ atoms ]<br>
H5T HO 0.44220 1<br>
O5' OH -0.63180 2<br>
C5' CT -0.00690 3<br>
H5'1 H1 0.07540 4<br>
............................................<br>
[ DG5 ]<br>
[ atoms ]<br>
H5T HO 0.44220 1<br>
O5' OH -0.63180 2<br>
C5' CT -0.00690 3<br>
H5'1 H1 0.07540 4<br>
H5'2 H1 0.07540 5<br>
C4' CT 0.16290 6<br>
H4' H1 0.11760 7<br>
O4' OS -0.36910 8<br>
C1' CT 0.03580 9<br>
...................................................<br>
<br>
<span style="font-weight:bold">But then also when I am running the file with the command:</span><br>
<br>
pdb2gmx -f dna5.pdb -o dnA5.pdb -p topol.top<br>
<span style="font-weight:bold"> with TIP3P water model</span><br style="font-weight:bold">
<span style="font-weight:bold">I am getting the following error:</span><br>
<br>
Identified residue DG51 as a starting terminus.<br>
Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA).<br>
Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA).<br>
Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA).<br>
Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA).<br>
Warning: Residue Na2 in chain has different type (Ion) from starting residue DG51 (DNA).<br>
More than 5 unidentified residues at end of chain - disabling further warnings.<br>
Identified residue DG51 as a ending terminus.<br>
8 out of 8 lines of specbond.dat converted successfully<br>
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn<br>
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn<br>
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.5.5<br>
Source code file: pdb2gmx.c, line: 655<br>
<br>
Fatal error:<br>
Atom OH in residue DG5 1 was not found in rtp entry DG5 with 31 atoms<br>
while sorting atoms.<br>
<br>
<br>
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Thanks in advance<br>
<br>
</div>
<div style="font-size:9pt; font-family:'Calibri',sans-serif">========================================================<br>
Anik Sen<br>
Student<br>
CSIR-Central Salt & Marine Chemicals Research Institute,<br>
Gijubhai Badheka Marg.<br>
Bhavnagar, Gujarat 364002<br>
<div><img alt="www.csmcri.org" src="http://www.csmcri.org/images/logo.png"></div>
========================================================</div>
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