[gmx-users] (no subject)

Sanim Rahman sanimr at mail.usf.edu
Sat Mar 18 05:37:41 CET 2017

Hi all,

I am trying to run grompp on POPC lipid bilayer that I constructed in
CHARMM-GUI. I originally input the whole assembled bilayer from CHARMM-GUI,
however, I received the error:

"No Default U-B Types"

>From a few previous threads, it was suggested that I stripped the waters
and use pdb2gmx on them separately in GROMACS. I did that and included the
#include command in my lipid topology file to reference water.itp. However,
I receive the following error:

"Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
while at->nr = 17152)"

This is what the end of my POPC topology file looks like:

*; Include Position restraint file*
*#ifdef POSRES*
*#include "posre.itp"*

*; Include water chain topology*
*#include "water.itp"*

*; Include water topology*
*#include "./charmm36-nov2016.ff/tip3p.itp"*

*; Position restraint for each water oxygen*
*[ position_restraints ]*
*;  i funct       fcx        fcy        fcz*
*   1    1       1000       1000       1000*

*; Include topology for ions*
*#include "./charmm36-nov2016.ff/ions.itp"*

*[ system ]*
*; Name*

*[ molecules ]*
*; Compound        #mols*
*Other               1*
*Water               1*

I recalled implementing the same technique in one of the GROMACS tutorials,
but I am unsure what I am doing differently in my approach to receive this
Thank you. I will truly appreciate your assistance.
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
Co-Founder and Co-President of the Undergraduate Research Society
Undergraduate Researcher, Global Center for Hearing and Speech Research

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