VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Thu Nov 29 2018 - 06:08:46 CST

Thanks peter the issue is resolved by adding qqq in segname.

On Wed, Nov 28, 2018 at 7:18 PM Peter Freddolino <petefred_at_umich.edu> wrote:

> Does your solvent pdb have segid QQQ for all solvent atoms? That is the
> most common point of failure for nonstandard solvents (see the notes in the
> solvate documentation at
> https://www.ks.uiuc.edu/Research/vmd/plugins/solvate/)
> Best,
> Peter
>
> On Wed, Nov 28, 2018 at 5:51 AM surya narayanan chandrasekaran <
> sonofsunsurya_at_gmail.com> wrote:
>
>> Dear all,
>> I was trying to build ice box around my protein using
>> solvate plugin and gui and always end up in one replica of my equilibriated
>> box. So here are the details i have ice box of TIP4P around 20 Angst and i
>> am trying to build around my protein always end up in single box its not
>> completly built around the protein.
>>
>> Here are the commands i have tried.
>> solvate prot1.psf prot1.pdb -s W -minmax {{-45 -45 -45} {45 45 45}}
>> -rotate -spsf ICES-hex.psf -spdb ICES-hex.pdb -stop tip4p.top -ws 23 -o
>> ice-prot -ks "name OH2"
>> ----------------------------------------------------------------------
>> solvate prot1.psf prot1.pdb -rotate -spsf ICES-hex.psf -spdb ICES-hex.pdb
>> -stop tip4p.top -t 100 -o ice-prot -ks "name OH2"
>>
>> and ice box is hexagon shape as ICE structure of water.
>> psfgen) reading structure from psf file ice.psf
>> psfgen) Unable to add (duplicate?) residue U:2
>>
>> ---------------------------------------------------------------
>>
>>
>> Warm regards,
>> Dr. Suryanarayanan C
>>
>>
>> 

-- 
Warm regards,
Dr. Suryanarayanan C