Oh, sorry, please read:
loadpdb prot prot.pqr
On Thu, Jun 9, 2011 at 2:56 PM, Azat Mukhametov <azatccb.gmail.com> wrote:
> By the way, it looks that loadpdb has problems with understanding of pqr
> files, when someone uses a command:
> loadpqr prot prot.pqr
>
> May somebody knows the more reliable way to read pqr into xleap/tleap?
>
> Thanks!
>
> On Thu, Jun 9, 2011 at 10:57 AM, Azat Mukhametov <azatccb.gmail.com>wrote:
>
>> OK, thanks much!
>>
>>
>> On Thu, Jun 9, 2011 at 10:50 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
>>
>>> There is a very similar command to "loadpdb" it is called "loadpdb" :)
>>> I don't think it reads in the charges from the pqr, but it should have
>>> the
>>> correct atom naming so that when you load the same parm set that you put
>>> in
>>> for pdb2pqr it should have the same charges.
>>> Give it a try!
>>>
>>> -Dan
>>>
>>>
>>> On Thu, Jun 9, 2011 at 11:35 AM, Azat Mukhametov <azatccb.gmail.com>
>>> wrote:
>>>
>>> > Hi All,
>>> > Does anybody know, is it possible to use PQR file produced by PDB2PQR
>>> to
>>> > prepare structures for MD simulation?
>>> > Is here any command like "loadpdb", but for PQR file?
>>> > Or any other way to perform conversion?
>>> >
>>> > Thanks!
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>>
>>>
>>>
>>> --
>>> Dr. Daniel J. Sindhikara
>>> Institute for Molecular Science
>>> E-mail: sindhikara.gmail.com
>>> Website: http://sites.google.com/site/dansindhikara/
>>> --
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 09 2011 - 00:00:05 PDT
