Re: [AMBER] Problem in loading the pdb file

From: Jason Swails <>
Date: Fri, 10 Jul 2015 06:49:46 -0400

> On Jul 10, 2015, at 12:39 AM, Harshala Haldankar <> wrote:
> Hi,
> Thank you Jason for your reply...
> I know its just a warning, but why does my xleap window shuts down
> automatically? It loads my pdb for few seconds and later Xleap window
> closes.

Ah, i didn't see that part. What is the last thing you see in the terminal that you started xleap from?

If you still don't get a message (like segmentation violation) then what does tleap say?

> Harshala Haldankar
> On Thu, Jul 9, 2015 at 4:28 PM, Harshala Haldankar <>
> wrote:
>> Hi,
>> I am doing lipid bilayer simulation (POPG/POPE) on my peptide (18-mer)
>> using AMBER14.
>> I am following An Amber Lipid Force Field Tutorial: Lipid14 Edition
>> According to the tutorial, I had used charmm gui to build the
>> protein/membrane system. After downloading the pdb at step5 from charmm
>> gui, I converted the pdb file from charmm to amber using
>> script. Now when I try to Ioad the converted pdb using
>> loadpdb command in xleap, I am getting "name change in pdb file residue"
>> (snapshot attached) warning and the xleap window automatically shuts down.
>> Can anybody please help me to solve this error.
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Received on Fri Jul 10 2015 - 04:00:04 PDT
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