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 - 02:42:35 CDT

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<<

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