[gmx-users] problem in running grompp

[Samik Bhattacharya]

hi
i am simulating a membrane protein in POPC bilayer and for that i am following 
justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing 
some problems in running the grompp command. after the solvation when i am 
going to run grompp, it is generting an error as follows    
''Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 843

Fatal error:
Atomtype CA not found''

but  is not CA the main chain alpha carbon...why is not grompp taking CA then? 
i can't make out where the problem lies? i little help on this shall be very 
encouraging.
Thank You
Shamik




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[gmx-users] problem in running grompp

[Samik Bhattacharya]

hi, i am simulating a membrane protein inside dppc bilayer and in this regard i 
am following justin's tutorial. but i ma facing a problem in running 
grompp...whenever i run it is giving error 

Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (1A68_genbox.gro, 49128)
 does not match topology (1A68.top, 48628)

now how to solve this problem? i have first generated the lipid box  with the 
protein then solvated it. i really need little bit of help to proceed to the 
next step...
Thaking You...
Shamik





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[gmx-users] problem in running grompp

[victor doss]

Hello,

when I run grompp  I get the following error message always. Whoever has  a 
correct fix to get rid of this error message and get the actual result,  Please 
suggest.

Thanking you


Dr. Victor A. Doss


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Re: [gmx-users] problem in running grompp

[Justin A. Lemkul]

Samik Bhattacharya wrote:

hi
i am simulating a membrane protein in POPC bilayer and for that i am 
following justin's tutorial.it's a nice tutorial and is really helpful. 
but i'm facing some problems in running the grompp command. after the 
solvation when i am going to run grompp, it is generting an error as 
follows  
''Program grompp, VERSION 4.0.5

Source code file: toppush.c, line: 843

Fatal error:
Atomtype CA not found''

but  is not CA the main chain alpha carbon...why is not grompp taking CA 
then? i can't make out where the problem lies? i little help on this 
shall be very encouraging.


If you're seeing this error, then you've done something wrong when combining 
lipid.itp with the Gromos force field file.


-Justin


Thank You
Shamik



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] problem in running grompp

[Samik Bhattacharya]

--- On Mon, 8/6/09, Justin A. Lemkul  wrote:

From: Justin A. Lemkul 
Subject: Re: [gmx-users] problem in running grompp
To: "Discussion list for GROMACS users" 
Date: Monday, 8 June, 2009, 4:47 PM



Samik Bhattacharya wrote:
> hi
> i am simulating a membrane protein in POPC bilayer and for that i am 
> following justin's tutorial.it's a nice tutorial and is really helpful. but 
> i'm facing some problems in running the grompp command. after the solvation 
> when i am going to run grompp, it is generting an error as follows  
> ''Program grompp, VERSION 4.0.5
> Source code file: toppush.c, line: 843
> 
> Fatal error:
> Atomtype CA not found''
> 
> but  is not CA the main chain alpha carbon...why is not grompp taking CA 
> then? i can't make out where the problem lies? i little help on this shall be 
> very encouraging.

If you're seeing this error, then you've done something wrong when combining 
lipid.itp with the Gromos force field file.

-Justin

> Thank You
> Shamik
> 
> 
> 
Thank you Justin for the answar. but now how to solve it? where should i make 
changes to correct that? pls let me know what to do... waiting for your 
answar
Thank you again..
> 
> 
> 
> 
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-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] problem in running grompp

[Justin A. Lemkul]

Samik Bhattacharya wrote:


Thank you Justin for the answar. but now how to solve it? where
should i make changes to correct that? pls let me know what to do...
waiting for your answar
Thank you again..


"CA" is not an alpha-carbon, it is a ffgmx atom type.  So, therefore, you have 
copies some ffgmx parameters into the ffG53a6nb_lipid.itp that the tutorial 
describes, probably from the ";; parameters for lipid-GROMOS interactions" which 
the tutorial clearly tells you to delete.


-Justin


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-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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