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On 12/22/2011 6:07 PM, priya thiyagarajan wrote:
<blockquote
cite="mid:CAEuVTxA1gxMRtcKjFfHWw6Q=gMuWPmOA8eaFrXUm8Bdexpxhfw@mail.gmail.com"
type="cite">hello sir,<br>
i dono what i did was correct or not. But i did it.<br>
please tell me what i did was correct or not,,<br>
i tried two different ways to generate my top file.<br>
<br>
<br>
first i did prodrg for my whole lipopeptide and got its itp . pdb
and gro file.<br>
then i included information about atomtype, bond, pairs ,dihedrals
from this prodrg.itp into charmm27 forcefield rtp.<br>
And also added DRG as lipid in residuetype.dat..<br>
then i tried <br>
<b>pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh</b><br>
<br>
but i got error as<br>
<b> No atom found in .rtp file in residue moleculetype.</b><br>
<br>
so i though of using pdb file obtained from prodrg as input and
repeated the step.<br>
But still i am getting the same error.<br>
</blockquote>
<br>
Please copy and paste actual input and output. I can't tell from the
above whether you have mis-reported what error occurred or failed to
follow the file format when you attempted step 1 of <a
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>
(or likely both).<br>
<br>
As Justin suggested yesterday, you should start with something
simple. Get PRODRG to make a topology and coordinate file for
glycine. Plan to name it something other than GLY. Convert that to
.rtp and get that working with pdb2gmx. Then add complexity. You are
trying to run before you understand much about walking yet.<br>
<br>
<blockquote
cite="mid:CAEuVTxA1gxMRtcKjFfHWw6Q=gMuWPmOA8eaFrXUm8Bdexpxhfw@mail.gmail.com"
type="cite">
<br>
second way<br>
i took one topology file generated for some protein and edited it.
<br>
and i included my prodrg.itp file using include mechanism<br>
then set box to that prodrg.gro file and added water. And used
that top file which i edited since it contain all information
about my pdb.<br>
even my SOL molecules got written in that topology file.<br>
then i viewed that proteinwater.pdb file using pymol.<br>
when i go for energy minimisation i got error <br>
<b>atomtye CH3 not found</b>.<br>
</blockquote>
<br>
Just about anything here could be wrong, including trying to use the
prodrg.itp in a topology that formerly used an inappropriate force
field.<br>
<br>
Mark<br>
<br />--
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