Thanks a lot Sir.<br><br><div class="gmail_quote">On Mon, Feb 21, 2011 at 15:26, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Bipin,<br>
<br>
The file residuetypes.dat is quite different from aminoacids.dat. You<br>
can paste the following into that file (first line is number of<br>
entries, followed by so many residue names):<br>
<br>
49<br>
ABU<br>
ACE<br>
AIB<br>
ALA<br>
ARG<br>
ARGN<br>
ASN<br>
ASN1<br>
ASP<br>
ASP1<br>
ASPH<br>
CYS<br>
CYS1<br>
CYS2<br>
CYSH<br>
DALA<br>
GLN<br>
GLU<br>
GLUH<br>
GLY<br>
HIS<br>
HIS1<br>
HISA<br>
HISB<br>
HISH<br>
HYP<br>
ILE<br>
LEU<br>
LYS<br>
LYSH<br>
MELEU<br>
MET<br>
MEVAL<br>
NAC<br>
NH2<br>
PHE<br>
PHEH<br>
PHEU<br>
PHL<br>
PRO<br>
SER<br>
THR<br>
TRP<br>
TRPH<br>
TRPU<br>
TYR<br>
TYRH<br>
TYRU<br>
VAL<br>
<br>
<br>
Groetjes,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Mon, Feb 21, 2011 at 8:47 AM, bipin singh <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>> wrote:<br>
> Hi,<br>
> Thanks for your suggestion.<br>
> While running the g_covar it is showing the error that aminoacids.dat is not<br>
> found, so i have copied the residuetypes.dat(which i seems the new modified<br>
> name for aminoacids.dat in current GROMACS version), then it prompts to<br>
> choose the group for least square fit, which is not usual groups(i.e protein<br>
> or C alpha groups etc.).....please suggest where i have made mistake.<br>
><br>
> Choose a group for the least squares fit<br>
> Opening library file aminoacids.dat<br>
> WARNING 2 [file aminoacids.dat, line 1]:<br>
> File aminoacids.dat is empty<br>
> Group 0 ( System) has 30585 elements<br>
> Group 1 ( GLU) has 47 elements<br>
> Group 2 ( HIS) has 86 elements<br>
> Group 3 ( ASN) has 224 elements<br>
> Group 4 ( PRO) has 56 elements<br>
> Group 5 ( VAL) has 272 elements<br>
> Group 6 ( MET) has 68 elements<br>
> Group 7 ( GLY) has 168 elements<br>
> Group 8 ( ILE) has 190 elements<br>
> Group 9 ( ALA) has 110 elements<br>
> Group 10 ( SER) has 143 elements<br>
> Group 11 ( PHE) has 80 elements<br>
> Group 12 ( LYS) has 242 elements<br>
> Group 13 ( TYR) has 189 elements<br>
> Group 14 ( LEU) has 304 elements<br>
> Group 15 ( GLN) has 102 elements<br>
> Group 16 ( TRP) has 48 elements<br>
> Group 17 ( ARG) has 120 elements<br>
> Group 18 ( ASP) has 108 elements<br>
> Group 19 ( THR) has 141 elements<br>
> Group 20 ( SOL) has 27882 elements<br>
> Group 21 ( CL) has 5 elements<br>
><br>
><br>
> On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
>><br>
>> Hi Bipin,<br>
>><br>
>> Try using a .gro or .pdb file as reference structure (-s). Only .tpr files<br>
>> are version specific.<br>
>><br>
>> Cheers,<br>
>><br>
>> Tsjerk<br>
>><br>
>> On Feb 21, 2011 8:05 AM, "bipin singh" <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>> wrote:<br>
>><br>
>> Dear GMX users,<br>
>><br>
>> I want to calculate the correlated motion between atoms during the md<br>
>> simulation<br>
>><br>
>> for that purpose I am using g_covar(the one which is available under<br>
>> <a href="http://www.gromacs.org/Downloads/User_contributions/Other_software" target="_blank">http://www.gromacs.org/Downloads/User_contributions/Other_software</a>)<br>
>><br>
>><br>
>><br>
>> but it is not compatible with the GROMACS-4.5.3, so please suggest me the<br>
>> alternative way or does anyone have the modified g_covar for<br>
>> GROMKACS-4.5.3.<br>
>><br>
>> --<br>
>> ---------------------------------<br>
>> Thanks and regards<br>
>> Bipin Singh<br>
>><br>
>><br>
>> --<br>
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><br>
><br>
><br>
> --<br>
> ---------------------------------<br>
> Thanks and regards<br>
> Bipin Singh<br>
><br>
><br>
> --<br>
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><br>
<br>
<br>
<br>
--<br>
</div></div>Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<font color="#888888">--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br><font color="#3333ff"><i><font face="arial, helvetica, sans-serif"><div>---------------------------------<br>Thanks and regards<br></div><div><span style="font-family: arial; font-style: normal;"><i><font face="arial, helvetica, sans-serif">Bipin Singh</font></i></span></div>
</font></i></font><div><font color="#3333ff" face="arial, helvetica, sans-serif"><i><br></i></font></div><br>