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On 6/04/2012 8:27 PM, rama david wrote:
<blockquote
cite="mid:CAD=-SYFuGWY_Fh5XGwFmvFSSYnk4L=+Gpkp6rCV_Uie+E3POwg@mail.gmail.com"
type="cite">Hi Gromacs Friends and Justin , <br>
<br>
Thank you for reply and suggestion.<br>
<br>
These is short part of my PDB . <br>
<br>
ATOM 1 1H ACE 1 0.000 0.000 0.000
<br>
ATOM 2 CH3 ACE 1 0.000 1.090 0.000
<br>
ATOM 3 2H ACE 1 1.028 1.453 -0.000
<br>
ATOM 4 3H ACE 1 -0.514 1.453 -0.890
<br>
ATOM 5 C ACE 1 -0.721 1.600 1.249
<br>
ATOM 6 O ACE 1 -0.839 2.806 1.453
<br>
ATOM 7 N PRO 2 -1.227 0.727 2.126
<br>
ATOM 8 CA PRO 2 -1.918 1.181 3.321
<br>
ATOM 9 HA PRO 2 -2.553 2.031 3.073
<br>
ATOM 10 C PRO 2 -0.928 1.587 4.404
<br>
ATOM 11 O PRO 2 -1.069 2.645 5.013
<br>
ATOM 12 CB PRO 2 -2.782 0.075 3.851
<br>
ATOM 13 1HB PRO 2 -2.469 -0.177 4.864
<br>
ATOM 14 2HB PRO 2 -3.822 0.401 3.862
<br>
ATOM 15 CG PRO 2 -2.645 -1.140 2.964
<br>
ATOM 16 1HG PRO 2 -2.232 -1.966 3.542
<br>
ATOM 17 2HG PRO 2 -3.606 -1.451 2.556
<br>
ATOM 18 CD PRO 2 -1.680 -0.755 1.882
<br>
ATOM 19 1HD PRO 2 -2.173 -0.830 0.913
<br>
ATOM 20 2HD PRO 2 -0.816 -1.419 1.895
<br>
ATOM 21 N GLY 3 0.076 0.740 4.644
<br>
ATOM 22 H GLY 3 0.135 -0.114 4.109
<br>
ATOM 23 CA GLY 3 1.083 1.012 5.650<br>
<br>
The gromacs96 53a6 .rtp file mention the following data...<br>
<br>
bondedtypes ]<br>
; bonds angles dihedrals impropers<br>
2 2 1 2<br>
<br>
[ ACE ]<br>
[ atoms ]<br>
CA CH3 0.000 0<br>
C C 0.450 1<br>
O O -0.450 1<br>
[ bonds ]<br>
C CA gb_27<br>
C O gb_5<br>
C +N gb_19<br>
[ angles ]<br>
CA C O ga_30 <br>
CA C +N ga_19<br>
O C +N ga_33<br>
[ impropers ]<br>
C CA +N O gi_1 <br>
<br>
[ NH2 ]<br>
[ atoms ]<br>
N NT -0.83 0<br>
H1 H 0.415 0<br>
H2 H 0.415 0<br>
[ bonds ]<br>
N H1 gb_2<br>
N H2 gb_2 <br>
-C N gb_9<br>
[ angles ]<br>
-O -C N ga_33<br>
-CA -C N ga_19<br>
-C N H1 ga_23<br>
-C N H2 ga_23<br>
H1 N H2 ga_24<br>
[ dihedrals ]<br>
-CA -C N H1 gd_14<br>
[ impropers ]<br>
-C -O N -CA gi_1<br>
N H1 H2 -C gi_1 <br>
<br>
As per my pdb file N atom is the part of PROLINE , not the ACE...<br>
I got the topology by using the Amber 03 FF.<br>
But my priority is to the GROMOS96 53a6 force field ...<br>
<br>
Could any suggest me the way to tackle these problem???<br>
</blockquote>
<br>
The default is to try to put termini on the protein chain. Your
chain already has them, so you need to tell pdb2gmx not to try to
add termini. See pdb2gmx -h.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAD=-SYFuGWY_Fh5XGwFmvFSSYnk4L=+Gpkp6rCV_Uie+E3POwg@mail.gmail.com"
type="cite"><br>
With Best Wishes, <br>
R.Davaid<br>
<br>
<div class="gmail_quote">On Thu, Apr 5, 2012 at 4:13 PM, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
rama david wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Gromacs friends,<br>
<br>
When I given the command ...<br>
pdb2gmx -f .. -o .. -p .. -ignh<br>
I gate the following error..<br>
<br>
------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.5.4<br>
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c,
line: 1070<br>
<br>
Fatal error:<br>
atom N not found in buiding block 1ACE while combining tdb
and rtp<br>
For more information and tips for troubleshooting, please
check the GROMACS<br>
website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
When I goes through the detail of the website at <a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a>
and document<br>
I come to know that I have to modify the rtp file,<br>
</blockquote>
<br>
</div>
Nowhere in the explanation of the error does it suggest that
you should alter the .rtp file in this instance. You have
atoms in your structure that are not in the .rtp entry.
Specifically, your structure file has an N atom in ACE, but
ACE only contains CA, C, and O. The N atom should be the
first atom in the next residue, not ACE.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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