On 4/22/13 5:30 AM, Baptiste Demoulin wrote:
Hi,
You have to add an entry for the DRG residue in "aminoacids.rtp", in the
gromos folder. Instructions on this can be found in the GROMACS manual
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
This is not correct. PRODRG produces a topology (albeit a very flawed one), so
there is no need whatsoever to modify .rtp files since pdb2gmx should never be
involved in this workflow.
-Justin
2013/4/22 zyduscadila <haresh.aj...@zyduscadila.com>
Dear Justin thanks for your email.
I have tried those you mentioned in your email.
I have submitted molecule of interest in PRODRG and got a DRG.itp or
DRG.pdb
file.
I fired command pdb2gmx using DRG.pdb (obtained from PRODRG) using Gromos96
43a1 force field , but I received the follwoing fatel error:
"Residue "DRG" not found in residue topology database".
Let me know, how to handle this error ? please give me a brief step how to
do this ?
I hope you will give me a solution. Thanks in advance
Thanks & Regards,
HARESH AJANI
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Only-Ligand-Without-Receptor-MD-Simulation-with-solvent-other-than-water-tp5007488p5007537.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
