The atom "names" are just arbitrary string labels. Many codes rely on this to uniquely identify atoms but that is really a rather dumb way of doing this. Antechamber will probably just simply construct those labels combining the element name with a running counter.
The mol2 files you have shown have the GAFF atoms types in the 6th column. So, yes, antechamber will construct force fields parameters on that basis (in fact, antechamber has created those on the basis of bond type perception and guessing the elements). It does not depend on atom labelling.
The PDB format is strictly column based that is all fields must start and end on a specific column. This is very well documented so please read the docs.
________________________________________
From: Hong Sun [sun530.purdue.edu]
Sent: 24 March 2016 03:57
To: amber.ambermd.org
Subject: [AMBER] questions about mol2 and pdb file.
Dear amber experts,
Hello,I am a beginner in amber.Recently I am following one tutorial "a Room Temperature Ionic Liquid" .I got two molecule pdb file from gaussian software.And then I transfer them into mol2 format using antechamer command .I notice that atom name in the mol2 file are not the same as the example mol2 file.For example,in acn.mol2 file I made(as follows) ,atoms is named by a element name followed by sequence number. The same to other molecule file.
1 N1 5.5860 -7.0430 0.0000 n1 1 ACN -0.375800
2 C2 6.6640 -6.0010 0.0000 c1 1 ACN 0.208700
3 C3 6.0430 -4.6350 0.0000 c3 1 ACN -0.045000
4 H4 6.9530 -4.2210 0.0000 hc 1 ACN 0.070700
5 H5 6.2300 -3.6530 0.0000 hc 1 ACN 0.070700
6 H6 5.0600 -4.4480 0.0000 hc 1 ACN 0.070700
But in the example acn.mol2 file,it shows like this way.
1 H1 2.0000 1.0000 -0.0000 hc 1 ACN 0.070700
2 C1 2.0000 2.0900 0.0000 c3 1 ACN -0.045000
3 H2 1.4860 2.4540 0.8900 hc 1 ACN 0.070700
4 H3 1.4860 2.4540 -0.8900 hc 1 ACN 0.070700
5 C 3.4270 2.6410 -0.0000 c1 1 ACN 0.208700
6 N 4.7330 3.2140 -0.0300 n1 1 ACN -0.375800
Besides,for the bmi.mol2 file,there exists some unique atom name such as ND1 and CE1 which I can not found in my file.I am curious about the naming method of this antechamber command.And will it bring something different in my calculation?Can it find suitable force field parameter for different atom name?
And I have made changes for atom name in the pdb file responding to mol2 file.It seems there is some specific requirements for the pdb format.For example,if I make a larger spacing distance between O1 and chc in the following file,it gave error information about not finding a proper residue name while I use loadpdb command.Is there some notation about the pdb file format?
6 ATOM 1 O1 chc A 1 43.509 12.032 1.280 1 0
7 ATOM 2 N2 chc A 1 40.618 10.274 2.915 1 0
8 ATOM 3 C3 chc A 1 41.379 11.316 2.081 1 0
9 ATOM 4 C4 chc A 1 40.144 10.886 4.195 1 0
10 ATOM 5 C5 chc A 1 41.465 9.063 3.224 1 0
11 ATOM 6 C6 chc A 1 42.849 11.601 2.450 1 0
12 ATOM 7 H7 chc A 1 41.404 10.902 1.071 1 0
Any help is very appreciated.Many thanks! Look forward to your reply.
Best,
Hong
Purdue University Mechanical Engineering
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Received on Thu Mar 24 2016 - 00:30:03 PDT
