Re: [gmx-users] dealing with ATP

2011-04-25 Thread Mark Abraham
m:* Justin A. Lemkul *To:* Gromacs Users' List *Sent:* Sat, April 23, 2011 5:46:24 PM *Subject:* Re: [gmx-users] dealing with ATP Sajad Ahrari wrote: > tnx for your help Justin! > but shouldn't the topology of S atom be described for gromacs? unless gromacs may know P atom with t

Re: [gmx-users] dealing with ATP

2011-04-25 Thread Itamar Kass
C4 N9 DONE STOP *From:* Justin A. Lemkul *To:* Gromacs Users' List *Sent:* Sat, April 23, 2011 5:46:24 PM *Subject:* Re: [gmx-users] dealing with ATP Sajad Ahrari wrote: > tnx for your help Justin! > but shouldn't the topology of S atom be described f

Re: [gmx-users] dealing with ATP

2011-04-25 Thread Sajad Ahrari
DONE STOP From: Justin A. Lemkul To: Gromacs Users' List Sent: Sat, April 23, 2011 5:46:24 PM Subject: Re: [gmx-users] dealing with ATP Sajad Ahrari wrote: > tnx for your help Justin! > but shouldn't the topology of S atom be described f

Re: [gmx-users] dealing with ATP

2011-04-23 Thread Justin A. Lemkul
cussion list for GROMACS users *Sent:* Sat, April 23, 2011 5:54:58 AM *Subject:* Re: [gmx-users] dealing with ATP Sajad Ahrari wrote: > Dear users > i am working with a protein witch holds a hetero-atom in it's pdb structure. the hetero-atom is named "d" and stands fo

Re: [gmx-users] dealing with ATP

2011-04-23 Thread Sajad Ahrari
users Sent: Sat, April 23, 2011 5:54:58 AM Subject: Re: [gmx-users] dealing with ATP Sajad Ahrari wrote: > Dear users > i am working with a protein witch holds a hetero-atom in it's pdb structure. >the hetero-atom  is named "d" and stands for "ADP+SO4" (in fac

Re: [gmx-users] dealing with ATP

2011-04-23 Thread Justin A. Lemkul
Sajad Ahrari wrote: Dear users i am working with a protein witch holds a hetero-atom in it's pdb structure. the hetero-atom is named "d" and stands for "ADP+SO4" (in fact the third phosphate of ATP is being substituted with SO4). i wanted to know if gromacs holds a feature to change "d" int