AMBER Archive (2009)

Subject: Re: [AMBER] Fail to allocate ff

From: Madhurima Jana (tinni.217_at_gmail.com)
Date: Tue Mar 03 2009 - 08:27:41 CST

Hi,

Thanks for the reply. Actually whenever I'm generating the frcmod file
for a single CCL4 molecule using antechamber, it shows no parameters
inside the file except the Characters headings (MASS, BOND, ANGLE,
DIHE, IMPROPER, NONBON). Whereas the mol2 file has been generated
successfully using this. So my query is if it is possible to create
the parmtop and inpcrd files for 900 molecule from that mol2 file? If
it then can you pls suggest me what will be the procedure ?

Thanks,
Madhurima

On Tue, Mar 3, 2009 at 6:40 PM, Nicholas Musolino <musolino_at_mit.edu> wrote:
> Hi Madhurima,
>
> I believe that for estimating partial charges, parameters, etc., antechamber
> works for single ligands. If you include more than one molecule in the MOL2
> file, antechamber will be confused.
>
> I think one approach that may work is to run antechamber with a single CCL4
> molecule, to get these parameters, and then create a system of 900 of them
> in tLeap. Think of it this way: you want partial charges and parameters for
> CCL4 _as a species_, and then you might happen to decide to simulate 900 of
> them, or 901 molecules, etc., later.
>
> Nicholas
>
> On Mar 3, 2009, at 6:17 AM, Madhurima Jana wrote:
>
>> Hi All,
>>
>> I want to perform a MD simulation of CCL4 box using AMBER force field.
>> For that I want to create the corresponding inpcrd and parmtop files.
>> Actually my system contains 900 CCL4 molecule in an orthorhombic box.
>> Using antechamber I was able to create a mol2 file for a single CCL4
>> molecule and from that the corresponding inpcrd and parmtop files.
>> But whenever I'm trying to do so for 900 molecules it is showing
>> following error:
>>
>> The atom number exceeds the MAXATOM, reallocate memory
>> Info: the bond number exceeds MAXBOND, reallocate memory automatically
>>
>> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
>> Total number of electrons: 66600; net charge: 0
>>
>> Running: $AMBERHOME/exe/divcon
>> STOP Error: Fail to allocate ff
>> Error: unable to find divcon charges in divcon.out
>>
>> Could anyone please suggest me how to overcome it.
>>
>> Thanks,
>> Madhurima
>>
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>
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