Re: [gmx-users] N-terminus type PRO-NH

Nguyen Hoang Phuong wrote: Is pdb2gmx recognising the N-terminal residue as PRO? I think so. However in my case pdb2gmx does not read the entry PRO-NH in the ffG43a1-n.tdb file. Only NH3+,NH2, or None are read. I cheat pdb2gmx by replacing the header [ PRO-NH ] by [ NH2 ] and it works for me n

Re: [gmx-users] N-terminus type PRO-NH

> > Is pdb2gmx recognising the N-terminal residue as PRO? > I think so. However in my case pdb2gmx does not read the entry PRO-NH in the ffG43a1-n.tdb file. Only NH3+,NH2, or None are read. I cheat pdb2gmx by replacing the header [ PRO-NH ] by [ NH2 ] and it works for me now. Phuong

Re: [gmx-users] N-terminus type PRO-NH

Nguyen Hoang Phuong wrote: Dear All, I would like to have the N-terminus type PRO-NH for my molecule. I saw this option is available in the ffG43a1-n.tdb file but pdb2gmx does not provide this option (only NH3+,NH2, or None are available). Does anyone know how to get this N-terminus type? Is

Re: [gmx-users] Non-zero system charge

Hi, Yes, both the charge and dipole corrections are applied automatically. Still, the uniform background charge is a bit unphysical, so for reasonably long simulations you might prefer to just add counterions with genion and create a neutral system instead - you can find more discussion ab

Re: [gmx-users] error in pdb2gmx step

True. I checked the files and found that CO was not described in any of them and I did take care of the replacement ot A with a blank.  Well in this case do I have any alternatives? Like other compatible force fields or modification of the existing one. Annie Albin. On 3/31/06, MGiò <[EMAIL PROTE

[gmx-users] hi

Hello friends again i have faced the problem this time i have taken the Hydrolase ( TRYPSIN BEFORE A HIGH DOSE X-RAY "BURN") .i have taken the pdb file. i have edited the pdb file in the text editor i have removed all the hetero atoms and and put them in the dundee prodrg server and collected the