Re: [AMBER] dlpc membrane

From: <jojartb.jgypk.u-szeged.hu>
Date: Mon, 14 Nov 2016 12:05:17 +0100

Dear Batuhan,
You are right, thank you but this is only a type (my mistake :().
The error message is:
Created a new atom named: C12 within residue: .R<LA 1>
Created a new atom named: H2R within residue: .R<LA 1>
.
.
.
And further for the whole LA tail.
Best, Balazs

Id├ęzet (Batuhan Kav <bkav13.ku.edu.tr>):

> Dear Balazs,
>
> You load the pdb file into "lipid" variable and then trying to set the
> box size and save the parameters for "system" variable. "System" should
> be "lipid".
>
> Best,
>
> Batuhan
>
> On 11/14/2016 10:45 AM, jojartb.jgypk.u-szeged.hu wrote:
>> Dear Users,
>> I planned to running an MD for DLPC (128) bilayer.
>> The structure was prepared by charmmgui, and the pdb file obtained was
>> convert by charmmlipid2amber.py.
>> Using the attached tleap file (only lipid) I was not able to generate
>> the parm7 and rst7 files.
>> For other lipid types the generation was successful.
>> I checked the /opt/amber16/dat/leap/lib/lipid14.dat file but I didn't
>> see any possible error between the naming scheme, maybe I missed
>> something.
>> What could be the problem, and how can i solve this problem?
>> Thank you for your help.
>> Balazs
>>
>>
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>
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Received on Mon Nov 14 2016 - 03:30:03 PST
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