Hello,
In tleap you would:
tleap -s -f leaprc.GLYCAM_06j-1
GLU = sequence { ROH 0GB }
check GLU
saveamberparm GLU GLU.parm7 GLU.rst7
saveoff GLU GLU.lib
saveMol2 GLU GLU.mol2 1
savepdb GLU GLU.pdb
quit
Greeting,
Hector.
PS: http://glycam.org/docs/forcefield/glycam-naming-2/
> Dear sir
>
> I have checked naming in amber manual but i didn't understand i have also
> checked naming in GLYCAM_06j-1.prep file but they showed only 0GA,1GA,2GA
> type but how can i put only single complete GLUCOSE.
>
> On Sun, Sep 10, 2017 at 8:36 AM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
>> Hi ,
>> There are specific residue names for each monosaccharide as defined by
>> GLYCAM FF.
>> Just see the manual what is the residue name for your case.
>>
>> Best Regards
>> Elvis Martis
>> Mumbai, INDIA.
>>
>> ________________________________________
>> From: Aashish Bhatt <aashish.ph16221.inst.ac.in>
>> Sent: 09 September 2017 20:32
>> To: amber.ambermd.org
>> Subject: [AMBER] Regarding Glucose naming
>>
>> Dear Sir/Ma"am
>>
>> I have problem in naming of monosaccharide. I have used name of Glucose
>> as
>> GLC. and also supplied leaprc.GLYCAM_06j-1 file. but it did not
>> recognize.
>> please let me know if there is any other way of giving GLC as input.
>>
>>
>> Thanking you
>>
>> Aashish Bhatt
>> Institute of nanoscience and technology
>> Mohali, India
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>
--------------------------------------
Dr. Hector A. Baldoni
Profesor Adjunto (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
-.First thinghs first, but not necesarily in that order.-
-.The theoretical approach these days can predict/show almost anything,
but the ultimate truth lies in the experiment.-
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Received on Sun Sep 10 2017 - 11:30:02 PDT
