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On 27/01/2012 9:50 PM, Anik Sen wrote:
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cite="mid:BDE9D87D31C781498280133FD1BE69A51DD29D8A@EXCHANGE.csmcri.org"
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<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0,
0); 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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0, 0); font-size: 10pt;">
<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>
</div>
</div>
</blockquote>
<br>
The third column here is the atom name, the fourth is the residue
name.<br>
<br>
<blockquote
cite="mid:BDE9D87D31C781498280133FD1BE69A51DD29D8A@EXCHANGE.csmcri.org"
type="cite">
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0, 0); font-size: 10pt;"> <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>
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</div>
</blockquote>
<br>
The first column here is the atom name, the second column is the
atom type. pdb2gmx has to be able to match atom names in the .pdb
file with those here, for the given residue. In your case, it can't.
You will need to rename the atoms in the .pdb file, somehow. When
you do, make sure you preserve the column formatting of the .pdb
file.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BDE9D87D31C781498280133FD1BE69A51DD29D8A@EXCHANGE.csmcri.org"
type="cite">
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font-size:10pt">
<div style="direction:ltr; font-family:Tahoma; color:rgb(0,0,0);
font-size:10pt">
<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>
</div>
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>
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