AMBER Archive (2008)

Subject: Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro

From: Alan (alanwilter_at_gmail.com)
Date: Mon Aug 18 2008 - 04:34:03 CDT

Hi John,
Let me see if I understood well your problem.

You want to run a simulation of a protein with a modified amino acid, right?

If so, ok, I am still thinking in a better way of automatising this
procedure for GROMACS (using a tool I've been developing:
acpypi.googlecode.com).

But given the current situation, I would advice you to create your new
residue and put it in the respective ffamber*.rtp (look also at *.hdb,
*bon.itp and *nb.itp) of ffamber ports. Then, with your original pdb
(modified to to amber dialect) you could have you system solvatated, ionized
and ready for GMX.

There's also the possibility of creating everything you want in leap and
then use amb2gmx/acpypi to convert to GMX top and tweak it a little to have
the specific water model you want.

I don't know how big is your system in the end but be aware that rdparm
(used by amb2gmx) is limited to up 150k atoms or 50k residues (acpypi has
not limits but computer memory).

Cheers,
Alan

On Mon, Aug 18, 2008 at 10:01 AM, Grange Hermitage <ghermitage_at_gmail.com>wrote:

> I was thinking develop just the protein in AmberTools, use amb2gmx to
> convert then solvate and ionize with the gromacs tools pointed at the amber
> ports of the relevant water and ion model.
>
> The reason I don't use the amber ports for the proteins is that they have
> novel residues.
>
> You don't happen to know another defined tool chain for going from quantum
> calculations to gromacs topology do you?
> John.
>
>
> On Mon, Aug 18, 2008 at 5:12 PM, Alan <alanwilter_at_gmail.com> wrote:
>
>> Good you saw it's hardcoded. Next step you realise it's not difficult to
>> tweak your top file to match tip4pew water.
>> Alan
>>
>>
>> On Mon, Aug 18, 2008 at 6:04 AM, Grange Hermitage <ghermitage_at_gmail.com>wrote:
>>
>>> The definition of the water model is hardcoded in amb2gmx.pl
>>>
>>>
>>>
>>> On Mon, Aug 18, 2008 at 11:58 AM, Grange Hermitage <ghermitage_at_gmail.com
>>> > wrote:
>>>
>>>> Hi all,
>>>>
>>>> when the following leap script (AmberTools 1.2) is executed and followed
>>>> by amb2gmx.pl, the .top file is suitable for TIP3P and the .gro is suitable
>>>> for TIP4PEW. The .top file knows nothing about EPW. Gromacs then remarks
>>>> that the nunber of atoms in the .top and .gro don't match. Is there
>>>> something amiss in the leap file? There are no waters in chp16.pdb .
>>>>
>>>> Thanks,
>>>> John.
>>>>
>>>>
>>>> source leaprc.ff99SB
>>>> WAT = T4E
>>>> set WAT.1 name "T4E"
>>>> loadamberparams frcmod.tip4pew
>>>> loadoff ions94.lib
>>>> loadamberparams frcmod.ionsjc_tip4pew
>>>> loadoff chk.lib
>>>> loadoff chd.lib
>>>> chp16 = loadpdb chp16.pdb
>>>> check chp16
>>>> solvatebox chp16 TIP4PEWBOX 5 iso
>>>> addions chp16 Na+ 17
>>>> addions chp16 Cl- 13
>>>> check chp16
>>>> saveamberparm chp16 chp16leap.prm chp16leap.crd
>>>> quit
>>>>
>>>>
>>>
>>
>>
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>> >>http://www.bio.cam.ac.uk/~awd28<<
>>
>
> 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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