[gmx-users] g_covar to calculate correlation of motion

[Tsjerk Wassenaar]

Hi Bipin,

The file residuetypes.dat is quite different from aminoacids.dat. You
can paste the following into that file (first line is number of
entries, followed by so many residue names):

49
ABU
ACE	
AIB
ALA
ARG
ARGN
ASN
ASN1
ASP
ASP1
ASPH
CYS
CYS1
CYS2
CYSH
DALA
GLN
GLU
GLUH
GLY
HIS
HIS1
HISA
HISB
HISH
HYP
ILE
LEU
LYS
LYSH
MELEU
MET
MEVAL
NAC
NH2
PHE
PHEH
PHEU
PHL
PRO
SER
THR
TRP
TRPH
TRPU
TYR
TYRH
TYRU
VAL


Groetjes,

Tsjerk

On Mon, Feb 21, 2011 at 8:47 AM, bipin singh <bipinelmat at gmail.com> wrote:
> Hi,
> Thanks for your suggestion.
> While running the g_covar it is showing the error that aminoacids.dat is not
> found, so i have copied the residuetypes.dat(which i seems the new modified
> name for aminoacids.dat in current GROMACS version), then it prompts to
> choose the group for least square fit, which is not usual groups(i.e protein
> or C alpha groups etc.).....please suggest where i have made mistake.
>
> Choose a group for the least squares fit
> Opening library file aminoacids.dat
> WARNING 2 [file aminoacids.dat, line 1]:
>   File aminoacids.dat is empty
> Group     0 (      System) has 30585 elements
> Group     1 (         GLU) has    47 elements
> Group     2 (         HIS) has    86 elements
> Group     3 (         ASN) has   224 elements
> Group     4 (         PRO) has    56 elements
> Group     5 (         VAL) has   272 elements
> Group     6 (         MET) has    68 elements
> Group     7 (         GLY) has   168 elements
> Group     8 (         ILE) has   190 elements
> Group     9 (         ALA) has   110 elements
> Group    10 (         SER) has   143 elements
> Group    11 (         PHE) has    80 elements
> Group    12 (         LYS) has   242 elements
> Group    13 (         TYR) has   189 elements
> Group    14 (         LEU) has   304 elements
> Group    15 (         GLN) has   102 elements
> Group    16 (         TRP) has    48 elements
> Group    17 (         ARG) has   120 elements
> Group    18 (         ASP) has   108 elements
> Group    19 (         THR) has   141 elements
> Group    20 (         SOL) has 27882 elements
> Group    21 (          CL) has     5 elements
>
>
> On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>>
>> Hi Bipin,
>>
>> Try using a .gro or .pdb file as reference structure (-s). Only .tpr files
>> are version specific.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Feb 21, 2011 8:05 AM, "bipin singh" <bipinelmat at gmail.com> wrote:
>>
>> Dear GMX users,
>>
>> I want to calculate the correlated motion between atoms during the md
>> simulation
>>
>> for that purpose I am using g_covar(the one which is available under
>> http://www.gromacs.org/Downloads/User_contributions/Other_software)
>>
>>
>>
>> but it is not compatible with the GROMACS-4.5.3, so please suggest me the
>> alternative way or does anyone have the modified g_covar for
>> GROMKACS-4.5.3.
>>
>> --
>> ---------------------------------
>> Thanks and regards
>> Bipin Singh
>>
>>
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>
>
> --
> ---------------------------------
> Thanks and regards
> Bipin Singh
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands