[gmx-users] re:Membrane Peptide+ DPPC+ Water simulation

[pandey at bioinfo.ernet.in]

Hi all,

Thanks for reply, John.:)

I have used the file provided by you. But, sadly I am still getting error.
The section of error message.

I have followed exactly, what you have said. Renamed the ffG43a2x.itp.

In general I am trying lipid simulation with following step:

1) Get dppc_npat, dppc.itp and lipid.itp from Prof. Tieleman site.

2) Get (i)ffG43a2x.tar
(which has following
files:ffG43a2x.atp,ffG43a2x-c.tdb,ffG43a2x.itp,ffG43a2x-n.tdb,ffG43a2xbon.itp,
ffG43a2x.hdb, ffG43a2xnb.itp, ffG43a2x.rtp)
       (ii)ffgmx_lipids.tar (which has following files:
ffgmx.atp, ffgmxbon.itp, ffgmxnb.itp, ffgmx.itp)

(3)use pdb2gmx, editconf, genbox command with appropriate parameter

4)edit *.top file with following:
either
(i)#include ffG43a2x.itp and #include dppc.itp
 or
(ii)#include ffgmx.itp and #include dppc.itp
(Note: In both cases i am getting error, which i have mailed in group erlier)
(5)The reason i am not including lipid.itp is two:
(i) The lipid parameters are already included in the ffgmx.itp and
ffgmnb.itp (that i got from untaring ffgmx_lipids.tar)
(ii)When i include, lipid.itp also,the error of "second directive comes"
(6) Get the *.itp file, provided by John, and rename it as ffG43a2x.itp.
(7) Run grompp
-----------------error while grompp----------
WARNING 7 [file "dppc.itp", line 229]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 8 [file "dppc.itp", line 230]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 9 [file "dppc.itp", line 231]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 10 [file "dppc.itp", line 232]:
  No default Ryckaert-Bell. types, using zeroes
Cleaning up temporary file grompppCgmTJ
Fatal error: Too many warnings, grompp terminated
------------------end-----------------

-----------------section of topology file-------
; Include forcefield parameters
#include "ffG43a2x.itp"
#include "dppc.itp"
[ moleculetype ]
; Name            nrexcl
Protein_A           3
--------------------end-----------------

Is there any more step to follow, please tell me. I doing lipid simulation
for first time.

Cheers
Pandey
-------------
Research Assistant
Bioinformatics Center,
University Of Pune,
Pune
India

> Hi,
> The reason why you are getting the atomtype LC3 error is that there is
> another file on Peter Tielemans web site called lipid.itp that you need to
> include into the non-bonding file which corresponds to the forcefield you
> are using (ie ffG43a2xnb.itp). The dppc.itp file refers to parameters
> within
> the lipid itself (bond length, angle, charges etc). All that you do is cut
> and paste the corresponding entries from the lipid.itp file into the
> correct
> non-bonding file. Another thing is that there is also a GROMOS9645a3 also
> with improved aliphatic hydrocarbon parameters. I havent look at this yet,
> but you may want to.
> Cheers
> John
>
>
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