[gmx-users] adding hydrogens to pdb file

[Justin Lemkul]

On 8/29/15 10:18 AM, Johnny Lu wrote:
> pdb2gmx of gromacs add hydrogen to the molecule.
> http://manual.gromacs.org/programs/gmx-pdb2gmx.html
>

...only if one constructs an associated .hdb entry for the molecule.  pdb2gmx 
isn't magic.

-Justin

>
> On Sat, Aug 29, 2015 at 9:58 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
>> Hi.
>>
>> reduce.exe seems not part of gromacs.
>>
>> http://kinemage.biochem.duke.edu/software/reduce.php
>>
>> On Thu, Aug 27, 2015 at 1:59 AM, elham tazikeh <elham.tazikeh at gmail.com>
>> wrote:
>>
>>> Dear GMX users
>>> i want to *adding Hydrogens* to my lig.pdb (for making lig.itp file by ATB
>>> server) in cmd program in Windowds, but i dont know the way of that?
>>> i know the below command is used for that:
>>> reduce.exe -BUILD lig.pdb > lig_h.pdb
>>> but i cant do it in cmd program
>>> i really appricite for any help
>>> elham
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>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================